With Batguard Annihilation Field activated, followed by Charge, this should cause a Biotic explosion

We shouldn't have to "make it make sense."  The fact that there's any doubt about whether this interaction is working as intended is the issue.  Ideally, there should be a consistency with which the powers describe and the way they interact.  Your explanation is supported by the gameplay mechanics, but it requires speculation on the part of the player.  Speculation that Charge deactivates AF (which isn't mention in the power's description) only when attacking distant enemies, and that when AF is deactivated in this manner, it doesn't not induce a cool-down period.  Overall, it's always better if a game is consistent with it's descriptions and that any exceptions are explicitly listed and that players do not have to speculate on how powers interact to avoid having to test specific interactions.

No because the Annihilation Field moves with you, you never collide with it.

I do miss that biotic explosion from jump melee as well but I think he would get a little op(-ish) if he could prime with his punch.

Overall, I think he's a nice character as is, tbh...

Edit: Always nice to see a seasoned player join BSN, welcome aboard!

But that punch ripples the space-time continuum. Unfortunately the rest of his body is still prone to incoming fireworks.

I usually just call it "tijd-ruimte continuüm" 🤓