1. This may not be possible to fix, but it appears that 1.1 and 2.0 track grids are not aligned when using a 1.1 blueprint in 2.0. A symptom of this is that I'll put down a blueprint for a legacy station, and the inserters that remove from the wagons sometimes land in the same place as the track, as if the track has shifted by one tile.
Thew weird thing is that track in 2.0 still aligns to the same 2x2 grid as I remember it doing in 1.1. For example you can't place a track that is parallel to and spans a chunk boundary so the track has one rail in one chunk, and the other rail in an adjacent chunk. So the 2x2 grid for old and new tracks appears to be the same. I'm confused.

2. Legacy rails and new rails don't play nicely together. Most notably, if you have a straight section of legacy track, trying to use the rail planner to bring a curve of 2.0 track to an intersection with the straight legacy track can result in an error if you "overshoot" the connection, something I do very regularly.
Rather than try to fix this, it's been noted in one of the FFFs that support for legacy rails may be removed at some time in the future. This makes perfect sense, I suspect that keeping them working has incurred some amount of technical debt that you'd like to get rid of eventually.
So to this end I want to be proactive about removing as much legacy rail as I can. I suspect it's not at all easy to try and convert from legacy to current, and in any case that could only be done for straight tracks. Rather than try to do this, would it be possible to add a scanner that will display legacy rails on the world map and / or main game view, so we can replace them ourselves.
Take a look at the Orphan Finder mod to see the sort of UI that this might have. As an alternative, assuming that legacy rails and 2.0 rails have different names, would it be possible to write a mod that will show legacy rails, possibly based on the ideas in Orphan Finder?