My intonation is weird

[Gasman]

That is absolutly false,

The 12th fret harmonic is always in tune with the open string no matter how the intonation is set, it's physics of the string. Also to have the harmonic exactly in tune you have to place your finger exactly on the right spot by a few millimeters, otherwise the note of the harmonic might be sligthly off.

The only good way to do it is open string vs. fretted 12th fret.

This is absolutely correct. If your 12th fret harmonic is not in tune with the open string, then either the tuner is faulty, you aren't hitting the 12th fret harmonic, or you have opened a portal to another dimension where earthly physics has no place.

Make sure the 12th fret harmonic is in tune (which should mean your open string is properly tuned), then fret the 12th fret. If sharp, you need to adjust your bridge saddles to make the string longer.

Back to the OP's original post regarding different tunings, you really will need a separate bass for each tuning if you want your intonation to be dead on without whipping out a screwdriver between songs. Basically, same string + less (or more)tension results in more/less bowing of the neck, which changes action slightly, yadayadayada. I suggest you intonate your guitar to the tuning you will play the most of and forget it.