I generally assume SRM and LRM ammo is the same within manufacturer, but often different between manufacturers. So, default is that Holly 5 and Holly 10 LRM use the same exact ammo, but that the Doombud LRM ammo is different unless I specifically decide they are manufacturing the same thing. AC ammo is almost always separated both by damage and manufacturer. I use a spreadsheet to track the ammo and parts inventory, and include when it was gained, how it was gained, and when it was used. Yes, it takes effort, but makes the campaign much more enjoyable for me.
Actuators, limbs, cockpits, etc. are generally specific to the mech type. A Whitworth and Phoenix Hawk shoulder may weigh and cost the same, but are not interchangeable. Myomer fibers and armor sheeting interchangeable. Replacing components and weapons with those from another manufacturer is rare, because the on-board computer has to be reprogrammed, and not everyone can do that. Just as important, even if the components weigh the same, they might be of different dimensions, and so can't be swapped out without a significant rebuild of the chassis.
I rarely use anything but standard designs. Real reason - customizing holds little interest to me or the friends I play with. In-universe reason - their techs are not good enough for major changes, and/or the pilots are happy with the standard design. If there is a customization, it is virtually always because they can't acquire the proper weapons, and must plug something of lesser value into the hole until they do. So, if a Cicada 3c loses its PPC, it might run around for a while with a large laser. And they aren't going to upgrade the armor or something else to maintain weight - it just run a little light, and maybe I'll let them run 2km/hr faster when going all out. Forget customizing the mech - they just want to get the whole thing in working order!