Yes, they are always rarer than their retail counterpart, for the very simple reason that sample copies are drawn out of production in 1X or 1XX units at most. How would a sample version be printed in larger quantities than a retail version? That makes no sense. It's the same principle for music albums, movies and games.
They come out of the same place, with a sticker somewhere and a mark on the inner ring of the disc(s). There are rare cases where samples differ in other ways, but those are very rare cases, like
Power Drift & Mega Drive, where the disc and the back insert are different.
What would be interesting to know is how they calculate how many sample copies to print. Is it a percentage of all printed copies, or a fixed number regardless of all printed copies? And do some albums get no sample copies at all?
For example, I thought more recent Castlevania albums had no existing samples with sticker, but then I saw a sample Curse of Darkness soundtrack (the Japanese double-disc release), so that was a bit of a shock. I guess most if not all albums, at least in Japan, have samples made, but it may be almost impossible to verify, imagine if they make only 10 or 20 of them, and if they get returned or destroyed like they should, then some albums may have no samples existing anymore.
Also today in a shop, I saw some 8 cm singles from Sony Music, they were all samples. They normally keep those on the shelf and give you a retail copy when you go to the cashier. This, or it's their last copies and don't care about the sample marking, although that would be strange, since annoying customers may notice and complain (rightly so to be fair).