"Small pop mergers" do not consider things like accepted cultures, religions etc because it's not "assimilation" or "conversion" per se, it's simply meant to be "these pops are so small or have such a minuscule impact on the game economy they are like a larger pop's rounding error, so we may as well merge the two so we have one instead of two pops to run computations on".
In the beta, we noticed that when pops first arrive to a new place due to migration, their initial size was often so small they'd be considered one of these "rounding errors" and get gobbled up by a larger pop, only to find that a few days later their buddies would arrive with a similar size that would also get gobbled up, and so on. The full release of 1.2.3 should make it so small pops that likely arrived due to migration - either due to the presence of a mass migration target for that culture or due to being a primary culture of one of the market participants - are exempt from being merged due to small size, as they will likely accumulate more individuals over time.
Generally speaking, any observable effect due to small pop mergers - for example, entire populations simply disappearing over time - should be considered a bug or balance problem, these functions are strictly meant to be housekeeping processes that have no measurable impact on game outcome.