I've done it before and saved 103%. (not on that level though.)
I'm afraid we can't believe you on this.̆ Unless you have a hacked version of the game, we know from the DOS games' disassembly (the program's code) that the lemming is never counted twice when exiting in the manner you describe--it doesn't work because the game doesn't update the number of lemmings saved until the lemming
fully disappears from the level as it exits, and as soon as that happens it won't be affected by nuking or anything else.
It might work in other platforms (Mac, Amiga, WinLemm, etc.) since I haven't checked those, but CustLemm obviously runs on DOS and is based off of the DOS game.