It's definitely not just you.
With a standard setup you will typically have the strings (action) lower on the treble (G) side, so it's not necessarily counter intuitive that the pickups may sound better, and better balanced, when they're slightly lower on the treble side too. If the pickup get too close to the strings, all kinds of nasty things can happen, like weird chorus-like "out of tune" overtones (especially in higher frets) that messes with your intonation, causes loss of sustain and even fret buzz caused by the increased magnetic drag from the pickups. The ideal pickup height will always depend on a number of things: Your choice of strings, your playing style, your preferred setup and last, but certainly not least, the pickup itself. Some pickups need to be higher, some pickups need to be lower and some pickups are far more forgiving about the pickup height than others.
I also agree that thinner strings can sometimes sound "fatter" than heavier gauge strings. Especially if you're playing fingerstyle close to the neck. Thinner strings generally vibrate with a bigger amplitude, which generally means a fatter tone. But thinner strings may also have slightly lower output and slightly less sustain. But there is no correct "one size fits all" answer to this. The "best" strings/gauges for any bass player will depend on you playing style, and on what kind of tone you're looking for. For example, when playing aggressively with a pick close to the bridge it can often be the opposite, with heavier gauge G-strings sounding more robust and better balanced.