Good proposal, including its details 1 and 2, to solve a very hard problem.
It's good even when no features get cut. Despite beta-test engine versions that last several months, level/tileset designers feel rushed to stay at cutting edge. It's good to have several years or forever to adapt a pack. Level pack owners can transfer maintainership 5 years down the road, and the new maintainer is still not rushed to fix deprecation issues.
Multiple animations for a single tile are also good. I believe that all gadgets should animate when idle, especially triggered traps and decoration.
As an alternative to deprecation, we should consider autocorrection: When the game/editor loads the forbidden loose flames, they're automatically deleted, and when we load the half-exit, it's replaced with the two-animation locked exit. But this covers only your use case #3. Autoremoval will silently fail on use case #1 (feature cut), that's very expensive, even if it's rare.
Other: Might this be useful for terrain too? Perhaps use case #2 from above is relevant to terrain as well.
Terrain changes needs a very good reason and happen rarely, but yes, they should follow the same deprecation process. Until you asked this, I thought the deprecation feature was designed for all tiles.
-- Simon