But that doesn't change the fact that what you call incentives aren't necessarily fungible behaviors for all involved. Changing residential location isn't necessarily a simple matter. Some locations are too expensive for many, some of them have lousy services, some of them have lousy schools. Changing jobs also isn't necessarily simple for a lot of people, and suggesting that people should just "get another job" as a justification for tolls may or may not be good policy, but it'd be ridiculously unpopular. Moreover, the idea that the jobs will necessarily move is also not necessarily likely to happen; they're not always location-agnostic anyway, and there'd be plenty of companies that wouldn't move.
It absolutely is a punishment if you start imposing tolls on people who aren't likely to be able (let alone willing) to immediately uproot/rework their lives in the hopes of future improvements. It's one thing to target things like tolls to contexts where there are viable, useful alternative modes, and to use those as part of a strategy for encouraging those and new alternatives. It's very different if you impose these widely, because that's when you run headlong into forcing people to make choices they don't want to make. It's not easy to decide to move from a chosen place to live, it's not easy to decide to change jobs, it's not easy for employers to just relocate, all of these things have costs, all of them have trade-offs, and if you just impose tolls by fiat, people aren't going to see that as an incentive to change, they're going to see it as an extra burden heaped on them. So, in real life, far from being an incentive towards better transportation, what you'd actually get from an overbroad policy (and I mean anything other than very, very targeted) is a whole host of angry, angry people who the politicians listen to. Telling people to eat their vegetables is a politically disastrous proposition, and while it's perfectly fine to lament that fact, we don't actually get to ignore it, because the drivers vote too.