Here's a list of all the vanilla missiles and thier cooldown times:
Spoiler
- Small - Reaper - 5 sec
- Small - Atropos - 1 sec
- Small - Hammer - 1 sec
- Small - Swarmer - 5 sec
- Small - Annihilator - 5 sec
- Small - Salamander - 25 sec
- Small - Harpoon - 1 sec
- Small - Sabot - 1 sec
- Medium - Harpoon - 8.25 sec
- Medium - Sabot - 8.75 sec
- Medium - Salamander - 25 sec
- Medium - Annihilator - 0.5 sec
- Medium - Pilum - 15 sec
- Medium - Proximity - 3 sec
- Medium - Reaper - 15 sec
- Large - Reaper - 15 sec
- Large - MIRV - 15 sec
- Large - Squall - 10 sec
- Large - Swarmer - 5 sec
- Large - Hammer - 5 sec
There are very clearly some missiles which are not going to benefit from bypassing thier cooldown timer because it's trivial and would probably be over by the time you reach to press <F> anyway.
The recharging of the missiles doesn't seem particularly relevant as FMR will work just fine with any missile (that recharges or not), so long as there's ammunition.
Salamanders are only unique in this regard because they are the only missile type which does not use ammunition counters.
However, FMR is atrociously bad with recharging missiles like Pilums. You don't get significant burst like rapid-firing Harpoons/Sabots, neither you get sustain of Salamanders.
Comparing a direct weapon to a suppression weapon is never going to make the latter look good.
If I modify a Harpoon pod to recharge, does that make it bad? It works exactly the same as it did before, only now for longer. FMR still has the same interaction with it so long as there's any ammunition left, which there always will be now. So why is that bad?
Is it the partial salvo thing?
Because that's not really an issue, more of a self-balancing mechanism for
bursty recharging missiles.
Even if you don't like that you can either change the recharge parameters to specify a higher number of missiles to load for each step, or just straight up remove the ammo counter (which might not be a bad idea for Pilum actually - just have them on the cooldown timer like Salamander).