Odd. I have some pretty thick padding in some of my PI bibs/shorts and I’ve never noticed any measurable difference in the way my saddle feels compared to my tri suit. Any difference should be 1-2mm at most, I would assume. Certainly not “half a centimeter”… I say no way on that. The chamois is going to squish down to a pretty minimal height when you put weight on your chamois via your sit bones, unless you are super light, and even then I question this difference.
As I write this, I just got back from a ride wearing thicker bibs, and I just checked–a few mm’s, at most, between the outside of the short and my bare skin (at the sit bone).
One thought came to mind… are you using the same shoes/cleats for both setups? That shouldn’t necessarily matter, either, but if the tri sole shoes were significantly thinner than your non-tri shoes (assuming you have different shoes), then maybe that is the issue?
If this really is an issue and not a placebo-type effect, then I suppose measure for both and put a small piece of masking or painter’s tape on the seatpost, mark it with a pen, and move the saddle up and down per that reference point when you ride tri vs regular shorts.