Just to get this out of the way, I think the Junk's stats are fine for having 5 burn. I honestly hate that 5 burn as much as some other people have posted about, I think messing with that layer of the game is probably not a great idea because most people (including me for transparency) are outright allergic to slow ships. I have to REALLY like something to go down to 7 burn base. That being said, I think minmaxing map layer logistics like fuel and supplies sucks, so I tend to favor stuff having "OP" storage. 5 burn is a huge downside, if it does get nerfed and I don't think it needs one, consider giving it at least 6 burn, especially since it cant use militarized subsystems. Having higher burn and lowered stats I think would be fine too.
Take another look at my suggestion:
-Junk should have "Compromised Storage" by default. Like ludds ships have "Ill-Advised Modifications" even if it been manufactured from your own heavy industry, it still can be restored for additional credit investment ofcource.
-Junk should have "Civilian-grade Hull" hullmod. It would make sence cause "Compromised Storage" cannot appear on non-civilian ships and also allow player to use "Militarised Subsystems" on it.
-Junk's burn speed must be reduced from 5 to 4 (Can be restored with "Militarised Subsystems").
-Junk's maximum crew decreaced from 2000 to 1200 (This is important, cause with "Compromised Storage" D-mod it would go down to 840)
-Junk's skeleton crew decreaced from 500 to 320 ("Militarised Subsystems" doubles skeleton crew so you still can use it with "Compromised Storage")
-Junk's fuel capacity decreaced from 2000 to 800 which is level of Prometheus II - max for vanilla's non tanker ship
-Junk should no longer have shield and recieve +50% of flux vent stats effectively making "Shield Bypass" hull mod from S&Wpack as built in. (i explained why in separate post)
What i suggest is actually a buff, i see Junk in two separate loadouts: Miner and Combatant.
Current problem is what you can fit it as combatant and still benefit from enormous storage, fuel capacity and spare crew space. At the same time combatant stays at the edge of being good and completely suck. It highly relies on player perks/skilled officer to be effective so it need a slight buff to it's combat stats, which "Militarised Subsytems" just provide.
I want this 2 builds to be more separate, you should use it as 100% mining barge fitted with Xi Large mining collectors, Maglev mining generators and with Hammer Barrage in it's large missle slot OR as pure combat ship with some additional cargo as bonus.
My rework idea based around "Compromised Storage" D-mod and "Civilian-grade Hull"/"Militarised subsystems hullmods.
If you planning to use it as combatant you most probably never gonna restore "Compromised Storage" since this D-mod belong to "magnificent 5" group of D-Mods what doesn't change expluatation costs, but at the same time doesn't corrupt any important in-combat stats. The secret is what other 3 of these "magnificent 5" (malfunctioning comms, defective manufactury and damaged flight deck) is fighter based ones - they can appear on Junk, because it have some Hangar Bays, but at the same time Junk clearly not a carrier and never rely on it's fighters. I literally put in his bays 0OP mining drones to use them as additional projectile catchers, thats about it. In my playthrough i replaced "Compromised Storage" to "Unreliable Subsystems" so there is still a breathing room, because you only need 4 D-mods to reach full "Junker's" perk potential (maximum additional ordnance points).
At the same time what about maximum crew nerf from 2000 to 1200? Idea is simple, you need spare crew because mining consumes some, alongside with heavy machinery and supplies. You don't really need that many for battle, few hundreds for in-combat casualties is enough. With "Compromised Storage" 1200 goes down to 840, "Militarised Subsystems" doubles skeleton crew from 320 to 640 effectively left us 200 crew members for in-combat casualties from hull damage. There is even more (380) if you have "Safety Procedures 3".
Last, but not least - fuel ammount down from 2000 to 800. Again, for mining 800 is more than enough to supply not only the Junk itself, but even a small fleet of auxilary miners/protectiong ships/cargo freighters, if you, for some reason, want to fly at the edge of the map to mine there - you can buy more specialised ships for your needs (tankers).
Now you start to understand? As combatant Junk will recieve slight nerf to it's logistic stats (-30% or -15% if you have "Sefety Procedures 3" Skill), but would you really care? You wanted combat battleship, you get it, as bonus here couple thousands of additional cargo - nice. But "Militarised Subsystems" would actually noticebly buff it's in-combat performance. Don't forget what my meme-vid based on lvl103 pilot what have all the perks, but, let be honest, without "Skilled-Up" mod you have tought decisions, as you mentioned in your post - this faction highly benefits from yellow skill tree. You also need skills for -25% fuel and supply consumption. So you can't just have every combat-related skill at this point even at max level and thats why Junk needs a buff.
"Militarised Subsystems" provide such buff
Apart from removing the penalties from a civilian-grade hull, and increacing maximum burn level by 1 (remember why base burn level should be decreaced by 1?) and reducing supply and combat readiness cost to recover from a deployment by 30% it will also:
-Increases armour by percentage 25/30/35/45
-Increases flux capacity & dissipation by 10%
-Increases max speed, acceleration, deceleration, max turn rate & turn acceleration by 10%
All these stats is very important for him, it have thin 500 armor, bad flux stats and horrible engine perfomance.
Additionally, if you planning to use Junk as mining barge then you should invest additional credits to remove "Compromised Storage" which is totally right thing because Junk the best or one of the best miners in entire modded game with possibility to turn it in to your flagship, but it's dirt-cheap vessel which is not right. It will pay for himself after few mining runs full of volatiles.