I changed a spindle type to a cartridge a couple months ago. My measurements were off a couple MM from what it was supposed to be too.



Are both spindles symmetrical? A=C
Even if they are, it'll change your chain line by 2MM. Not a major amount. Cog spacing is close to 5MM, depending on how many cogs in your cassette.
If they aren't, use the end that matches up best.
BTW, it seems they don't match up perfectly anyway. I guess a crank that's been on/off a few times may have a bit of wear plus machining tolerances etc. With that slight of a tapper, ,001" difference on the "square" is going to allow a "few" .001" difference in chain line.