The mod system isn't a good reason to avoid the Moto Z lineup, because it's not at all necessary to use it. The only mod I have (aside from a couple style backs) is the first gen speaker, and I rarely use it. The Z Force is a very good phone without any mods, so there's no reason to buy them unless you want to, and no reason you'd get "locked in" to one phone line.
Tempered glass screen protectors are abundant and cheap, so the screen scratching isn't really an issue either, unless you just absolutely hate having a protector.
I too was burned by the lack of follow-through on promised updates (Droid MAXX), but so far Lenovo is doing pretty well with updates to the Z's. It's June, and we're on the May security patch. The June patch only just rolled out to Nexus/Pixel last week, so we're only just barely behind the bleeding edge on security updates. We're on Android 7.0, so not the absolute latest, but pretty good. So far I'm pleased with the updates, though we'll see how Lenovo does in the 12-24 month age span where support tends to drop off from most manufacturers.