The solution is surprisingly simple: increase the maximum ammo capacity of the lasergat to 1100, which is what it'd be with all perks. With no perks, it will still just reload to 500, and with partial perk acquisition with regard to fusion cores, it will reload to the calculated level all the way to all pertinent perks at 1100. Only minor bug is acquiring one of the perks while the lasergat is equipped; the change doesn't immediately reflect in the loaded core, but reloading in such a state from a fresh core will not redeposit the extracted core as slightly used.
Fix discovered after finding this mod and testing for myself: http://www.nexusmods.com/fallout4/mods/14689?
Chat log of my testing from Discord AFKMods UPP channel:
> > Gonna try that out myself to see if it does that. Got myself a lasergat on a heavy rack in the Castle armory and way too many fusion cores, as well as at least the Repair bobblehead.
> Yep, it's as simple as boosting the lasergat's ammo capacity to fix that bug.
> I had the Repair bobblehead and one Nuclear Physicist perk and it was 687. Dropping the saved up perk I had into a second level of Nuclear Physicist raises it to 825.
> Dropping the second perk point in doesn't immediately boost the lasergat to 825 if you have the lasergat equipped at the time of perk acquisition, but reloading will not deposit a slightly used fusion core in inventory.
> Discharged 22 times. 803/825 = 0.97333repeating. Reloading a new core deposits the slightly used core at 97% remaining charge.
> Now for a different test... discharging, plunking Nuclear Physicist 2 perk in, and *then* reloading. 668/687 charge comes to 0.972numberbarf
> Aaaand still puts a 97% core back in your pocket.