Increasing driver count is typically for two reasons. One is what Matt covered, where multiple drivers output the same frequency, so you get more amplitude without pushing the drivers as hard. Or, you can assign them each different frequencies, have better coverage over the entire range and have finer control over it as well. In the latter, think of the drivers like points or faders on a parametric EQ. The more points you have, the finer control you get over your EQ. So, rather than only having control over the lows and highs in a dual-driver IEM, you can manipulate the lows, mids and highs in a triple-driver. It allows the designer to EQ the IEM more precisely.
The possible decrease in clarity you're talking about may be referring to phasing. When you have drivers outputting different frequencies, there's a possibility that some of the frequencies they're outputting may overlap. For example, where the bass driver ends may slightly overlap with where the mid driver begins. Now, if those frequencies are misaligned in the time domain - meaning, they don't reach your ears at the same time - they may destructively interfere and do funky things like cancel each other out, resulting in an unfocused, often hollow sound. That's what may cause incoherence or unfocused-ness in multi-driver IEMs, but they're so advanced and their designers are so skilled now, that you're very unlikely to see phasing in a renowned brand like 64 Audio.
The Fourte and Trio's drivers are all tubeless, which changes their properties by quite a bit. I wouldn't be surprised if they were able to resolve and perform at a higher ability than most multi-driver designs. So, they don't need the extra headroom that stacking gives. Although they have relatively low driver counts, what drives their costs up is the R&D invested into the acoustics around them. Because they're open drivers, they radiate freely, and you can't tune them like you would a closed, spouted driver. You can add dampers and manipulate the length of sound tubes to shape the frequency curve of a traditional driver, but those options are obviously unavailable for a tubeless driver. The way to tune them would be similar to speakers, where you house them in a calibrated chamber that acoustically boosts wanted frequencies and dampens unwanted ones. The time and money taken to make all that work is what you're paying for when you get the Trio and Fourte, and it's what results in the performance that a lot of people have continuously raved about.