It is boosting the base value by the listed percentage. This is a similar situation to Warframe health mods and such, which don't take the leveling increase into account. I think the boosts from the parts should be incorporated into the base value, but it is consistent right now.
Railjack has its own bindings screen that starts out mostly blank. Reset that one to defaults. You should also check the main one for any blanks. I lost primary fire, alt fire, aim, and the up/down archwing controls.