I don't know if this will help but in my experience of playing both instruments the concept of tuning temperaments enters in to this discussion. The electric bass or any fretted instrument is in equal- temperament tuning but the upright is temperament-adjustable. Even the lines on a fretless are in equal. To me this means that there is literally no one spot on the fingerboard that is in tune all the time in all circumstances. Different strings have different overtones so that placing a finger directly across two strings may not sound in tune. Tuners are in equal temperament so the overtones are not necessarily in tune. The other instruments you're playing with affect it among other things. If you were ever in the unlikely situation of playing electric bass with a string quartet you would hear this immediately. Even if you're playing with a keyboard which is in equal temperament you would have to adjust your pitch on the upright compared with playing alone. There are many more aspects to temperaments and the whole subject is fascinating, at least to me. There are some excellent books on the subject but the ears really are the thing. IMO if you let go of the one-spot idea and get used to making hearing-based adjustments you save a lot of time and grief. Playing on or with only fixed pitch instruments like keyboard of guitar gives a limited and somewhat false idea of what good intonation is.
Again, respectfully, I understand all this. My fretless basses do not have "lines". I understand equal temperaments. I do make adjustments for temperaments, most obviously to third intervals, because they are usually the most egregious situations to deal with. I do this by ear, any other way would overload my brain. If I thought about it case by case, I could do it logically, but not in a musical flow.
Having said all this, the situation I find myself in with regards to the original subject is outside the bounds of a discussion on temperament. What I'm experiencing is an observation of greater magnitude than that. And it is inconsistent from string to string. The D vs G string discrepancy is "huge", but there is an opposite D to A string discrepancy, and really no E to A string discrepancy to speak of.
It's got to be a bum string or a problem with this particular model/brand of string.
So a final comment is this. I truly appreciate the spirit of all the answers here. This is a great forum and I'm grateful for it. If I reacted strongly, it is because I felt that certain folks weren't actually paying that much attention to what I was actually asking. I guess that is understandable, and I should be more patient. No one here knows me, so it is easy to jump to conclusions about how I might be misunderstanding a situation.