It looks like some ground tiles aren't being replaced like you mentioned.
I took a quick look at the code again. There appears to be a list of tiles that may be replaced in the code (to prevent concrete and bricks from being replaced I suppose). It already includes support for Alien Biomes, but it might be outdated. It shouldn't be much work to fix this, I'll probably look into it soon.
Or, in case you want to fix the issue yourself, feel free to create a PR on Gitlab. The list of tiles can be found here: https://gitlab.com/Danacus/surfaces-redux/blob/master/script/const.lua
Thanks for reporting the issue.