My intra-Schengen travel experience from last Sunday, fwiw
Taking a scheduled bus from Strasbourg (France) to Freiburg (Germany)… German border control spent half an hour scrutinizing everyone’s passport. We’re still on British passports as don’t even have PT pre-approval yet. Two border agents wanted to see all exit/entry stamps. They also gave a few other passengers similar hassle.
We originally planned to make this journey by train, but Sundays = track maintenance, hence the bus. I’m told trains don’t stop for these border checks, nor do cars (as was our experience driving Switzerland > Germany > Austria > Switzerland this summer), nor do people just walking or taking the tram from Strasbourg that crosses the border into Germany.
…and the bus trip back from Freiburg to Strasbourg? We didn’t even pass a border station, much less stop at one.
So in short, you take your chances with 90/180 days when crossing Schengen borders. But Germany seems to pay close scrutiny to buses coming over from France, Austria, etc. these days.