Okay so I've done some testing with 4.0.5 and here are my results:
Central Park (lvl 3): I can confirm jugato's observation, it takes me 3 refreshes for it to properly refresh. 1st one doesn't spawn clutter, second one spawns the swing twice, third one and further work as intended.
Toupee Shack (lvl 2): working as intended, the bed is now spawning as it should, aside from that the plot was working anyway (for me at least).
Scrap heap (lvl 3): working as intended now and I only needed to refresh once instead of 3 times like for the checkpoint.
Dead End Weapons (lvl 3): Refreshing the plot 4 times fixed it for me. First refresh doesn't spawn any clutter, second spawn does spawn some of it, third spawns all clutter but the turret on top gets spawned twice (just like with the lvl 3 checkpoint) and 4th refresh spawns everything and only one turret.
Outdoorsman: Still has issues, but I've found a rather tedious way to fix it. So my case is that I have a level 1 outdoorsman plot which upgrades to level 2 when I try to refresh it, it was that way since 4.0.0. Instead of properly upgrading to lvl 2 it just becomes stuck however. The first refresh does absolutely nothing and it stays at lvl 1, the second one de-spawns all the objects as well as the building itself and only respawns the lvl 2 bed, but nothing else.
The 3rd refresh spawns the lvl 2 bed + lvl 2 clutter objects, but still no building itself, so the objects are all floating in midair.
4th refresh and any that follow simply despawn all the objects and only the bed sporadically spawns again, but nothing else. I tried with both the Immersion Breaker Breaker as well as selecting the plot refresh option from the ASAM sensor, made no difference.
I also tried changing the building plan to another, then waited for it to finish building, then switched back to the outdoorsman building plan. Level 1 of outdoorsman builds just fine, as it already did with previous versions of SS, but using the console command "cf unlocklevel" to upgrade the plot to level 2 (for testing purposes only of course) also doesn't work. The scaffolding appears properly and the construction sounds are playing, but it never starts de-spawning the lvl 1 objects or spawning in the level 2 ones, even after several minutes of waiting.
So whether I simply refresh the plot or build a new one and try to upgrade it, it doesn't work properly.
Now here comes my "fix", if you refresh the plot ~3 times while it is stuck in the upgrading process, it does finish upgrading to level 2 and spawns in all the clutter objects as intended and can be refreshed without problems. This only works if you build a new level 1 plot (or switch to another plan and back, which is essentially the same) and upgrade it to level 2, an existing plot such as mine can't be fixed that way and the normal upgrade process still doesn't work and needs to manually be refreshed 3 times.