Pearl/opalescent mediums are, if memory serves, generally a mix of acrylic medium and mica powder. The mica is relatively coarsely ground, compared to paint pigment, in order to provide sufficient reflective surfaces. Because they're also intended to be mixed with fluid acrylics (craft paints, more often than not, but there are also hobby/model offerings), they are sometimes a bit on the thick side, themselves. Water and/or flow improver would be blanket recommendations for miniature work, but you already seem aware of that.
If a large batch works fine but a small batch clumps up, it sounds like there may simply be issues in mixing. If you make sure that both the medium and paint are thoroughly blended before mixing the two, there's no real difference between making 1ml, 10ml, or 500ml, aside from the difficulty in eyeballing the ratio and depositing the right amounts. It can be easier to stir a large batch than a tiny one, but measurement is often the greater rub. If you're mixing at a scale where you measure in whole drops of paint, I would think you'd be fine.
A little wastage is a small price to pay for a mix that actually works how you want it to. Hobby supplies aren't cheap, but it's not liquid gold we're talking about, either. While bad technique can make things worse, I think a degree of the issue is just to be expected. Trying to get exactly the amount of paint you need and no more, when talking about single parts, usually is more trouble than it's worth. Painters rarely end with clean palettes, after all. We can't
all just be that careless
