That's how it's supposed to work yet either one fitted will actually give you the bonus at the moment even though it's not supposed to!!
Fitting plasma beams but having the Ambiplasma console fitted will still give you a DPS bonus although it shouldn't! Swap it out to the correct one (the Plasma Infuser) & you'll get the same bonus increase!
Tried this with various beam damage types & corresponding consoles & the same thing happens.
Also tried with projectiles & the same results.
Bug report has been sent so expect it to be fixed at some point but it's been like this for over a month so far.. maybe longer!