Hmm - looking at the code, the number of motherships isn't random, but rather based on the number of constellations in the Sector, and that's fairly consistent. At the normal Sector size, this generally works out to 2 motherships, but it's capped to at least 1 and at most 3, to account for a smaller Sector size, mods, etc.
Having more motherships also isn't going to eat into the number of Remnants, at least not significantly, since both get an equal share of the available constellations.
As a sanity check, opening up my last 3 new games at random, each has 2 motherships. (If you press Ctrl-Z to disable sensors in devMode, then open the map and turn on star names, mothership stars are a flat red.)
A quick rundown of a typical vanilla Sector gen deciding how many motherships there should be:
The "derelicts" theme generator goes first. There are 52 constellations (this number can vary a bit), and it's allowed to use a third of them (the rest being reserved for other themes, i.e. REDACTED etc). So: ~17 constellations.
Each mothership requires an average of 13.25 constellations (for itself, and related probes and survey ships that chain towards it). So: 17/13 = ~1.3. The game rounds this up to 2. Thus: 2 motherships. If the number were >= 2.5, you'd get 3 motherships. To get 1 mothership, you'd need to have less than 40 constellations, which seems pretty unlikely (maybe impossible?) unless you're using a small Sector size.
