The problem with that is that exits may end up looking weird, due to being half no-effect object... I think though, especially with the long-term plans to merge them anyway, the pros outweigh the cons.
In regards to the Freedom Planet tilesets and L3 Egyptian / Shadow, the problem here is that the author is neglecting to update them, preferring to work on new tilesets instead (and then still targetting the old NeoLemmix version with those). I am not going to make adjustments to NeoLemmix specifically to accomodate people who refuse to upgrade; the only reason the old version should be used anymore is to preserve older content that cannot work on the newer one (packs with ghosts, Cheapo conversions, etc). However, the Shadow set case (and other similar ones, potentially) do a good enough job of justifying this, I think.