For all the Atlas lovers, I have only two words:
Difficult Terrain.
Assuming you've found ADF at all, which is not guaranteed in the first few months. And even with ADF you absolutely cannot reach that comfortable 19-20 burn level only base 10 burn ships can provide. For that reason alone my freighter of choice would always be Buffalo (P), not matter how far I'm into the campaign.
Allow me to make a few examples of my usual reasoning:
1) Early game I prefer exploration/Galatia missions, thus reaching the target system a few days earlier allows me to make an extra quest or even two. Putting Atlas in a fleet means a single Dram is no longer enough. I need at least Phaeton now, lowering average speed and agility on the campaign map even more, which often leads to otherwise avoidable fights. And traveling via storm clouds becomes really, really tough due to increased supply cost of bigger ships, which lowers average burn even more or eats up supplies at insane rate.
Meanwhile a single Buffalo can carry all the good, valuable stuff you actually want to haul back, has 10 burn, has Shielded Cargo holds for braindead bulk trading at black market with no risks involved. A-and will probably survive a retreat battle if all else fails. After all, it has enough spare OP for UI and a bit of flux capacity.
2) Mid-game is usually a time to found a colony or two, and babysit them for a few years, scanning nearby systems, farming ordos, developing contacts and doing bounty quests. Don't need much cargo capacity here either as I'm operating near my home base and, most likely, Core Worlds. Also there is no need to haul anything back as a commission and a few colonies will provide enough funds for any project I can think of. Buffalo is still king.
3) Late game the only items in your cargo should be around 100 machinery, token 20-30 transplutonics/volatiles for skill activation, and supplies. There is absolutely no need to have bigger cargo, no matter what you do or where you go. A single S-modded buffalo still provides enough space for half a year worth of supplies, assuming an efficient ~240 DP combat fleet and a few salvage rigs in tow.
All the above includes switching from Industry skills to combat skills at midgame, probably even earlier. If you keep the yellow tree it's even more relevant.
In all honestly, it's completely beyond me why anyone would want to lug around that huge, ugly brick of a ship. For me at least Starsector is too casual and unbalanced (read easy) to necessitate hauling anything but supplies and the most valuable loot.
Spoiler
Unless you're just space truckin' in the Core Worlds, which begs the question "why Starsector and not ETS2/Elite/X series/dozens of better simulation games".