A very valid observation there, Michael.
I normally use 1 guitar for each tuning. Now hold on, I know that might sound a bit extravagant, but my reasoning is this.
You are right when you talk about Standard tuning suiting the strings, as it were. So when you tune down, the strings should match the intonation.
I use a guitar especially for DAGDAD, one for Standard, and so on. Depending on the gauge that you feel comfortable with, compensation has to be made to keep the gauge in proportion to the tension. I use '60's for my bottom D, and '17's for my top D. I do like heavy guages, you understand. But it is in proportion to what I use for standard tuning, ie '58's for my bottom E, and '15's for my top E.
You may prefer lighter gauges, but there is a limit to which a string can be tuned down befor you start losing pitch on the fretboard.
If you're using one guitar to accomodate all your tunings, well then compromises have to be made when you select your gauges.
I change my strings every night when on tour, once every couple of weeks when I'm home. The important thing about new strings is to stretch them well before tuning them to pitch; they don't tend to go out of tune as quick.

I hope some of this makes sense. It works for me, anyway.

B.