The spacing of score elements has shifted from 3.5.2 to 3.6

A number of details of layout have indeed been improved and this could occasionally cause a measure to shift. In your examples, a fix was made to the stem lengths which were too short previously (in some cases not even even long enough to reach the notes!), also a change to tie thickness, also to how ledger lines widths are factored into layout. Offhand, I can't say which is responsible for any shifts here, but this sort of thing is to be expected in general.

Looking at this further, the most obvious difference to me is the space after the barline before the first note, which has increased in your PDF.

But I find I am not able to reproduce this difference. When I load into a current 3.6 build, keep the old style in the import dialog, and export the PDF, I get virtually the same spacing. The only visible difference is to the stem length. If on the other hand I elect to reset all style settings to the new defaults (in Format / Style), I get of course much bigger changes, but the relevant one is that the note left margin does indeed increase to 1.3 sp instead of 1 sp, which looks to be about the change I expect based on your example. So it looks to me like your PDF is using some but not all of the new defaults (it's obviously not Leland, for example). I also note the change in slur thickness in your PDF that would only happen if you accepted some but not all of the defaults.

So it's possible what you are seeing is an artifact of somehow getting the wrong style settings, either because you inadvertently accepted new defaults, or because of a bug in the style setting code that was present in the build you tested but has been fixed since (there have been a number of such fixes since the RC).

If you can still reproduce this in a current build, please give us the precise steps you are following with respect to how you open the file and how you respond to the import dialog, and tell us what setting you see for "Note left margin" in Format / Style / Measure.