I would never attempt to set intonation with anything other than utterly brand new strings. It's just too easy for organic contamination (you, chicken grease, etc.) or the windings shifting, etc., to pull off your readings. Magnetic pickup interference is generally not a problem with bass pickups, though I have heard of guys having them high enough that they'd gain a 'false fret' on the pickup shell if they played waaayyyy up the neck . . .
You say you're satisfied you've done the setup properly, so you have no obvious string rattle, fret interference that's audible, your heights are correct, and so on. So I'd reasonably expect there's no obvious problems on that front.
There will always be a disconnect with striking the compromise mathematically that a 'tempered' tuning requires. THAT discussion requires big-brain-processing that's way past me, except to acknowledge it since some guys and girls can just hear where it's 'off' even when everything is exactly right under this format we all work under. Having worked with more than a few pedal steel guitar players (the ultimate fretless instrument) who have to deal with an instrument that when they raise or drop notes, those also have to be in tune, and the great-ears players learn to live with the oddly in-tune/out-of-tune reflex it engenders.
I CERTAINLY don't have ears like that. I could never adjust intonation by ear, and if you can, I'm amazed. I always have to do it by strobe tuner. You can get really fussy about it, do your match/comparison adjustment at the 12th, then the 24th, etc., out several harmonics if you feel better about it that way. I would not approach it from the standpoint of measuring string lengths from a rule. I believe you could do that IF you were using four single wires that were identical: Add in different core sizes, different wrap diameter/ tensions, it would take lots of geometry to find out the optimum string length for a given scale. Use your tuner !
Remember also, identical string guages from different sets will adjust differently to be in tune. A 45 G from a roundwound RotoSound set is a different animal from a 45 G from a different brand, or even another 45 G from a different RotoSound product.
In a practical sense, I've never worried a whole lot if they were out just a bit: I never played chords on a gig(!) and I could never tell I was 'off' to the rest of the brand. So I'd advise play what you got, run them through a strobe and intonate them as best you can for now, finish the strings you have on. Then when you do change strings, you get it right at that time.
It's like instrument flying: I can't trust my ears, I have to trust the instruments (my faithfull BOSS tuner).
J o e y