We added the tag 'Coastal' to polders in the same way Moai and Feitoria have it listed. I am not 100% sure, but I believe it is meant to allow them to be built on tiles ONLY when those are also on the coast.
So, if I am following you, the problem is the non-removal of jungle/forests when constructing the polder, not the other terrain types.
If so, I agree, it does make it strange that that isn't a prerequisite to construction and yes, though small, the yields from tundra/desert is still better than unimproved.
I think this may be the result of a vanilla oversight.
The other BUILD types, farm, camp, plantation etc. all have a reference in the table BuildFeatures which describes which tech is necessary to clear the feature and time it takes to do it and how much production you get from it. Polders don't appear in this table.
So for instance, if you want to build a farm and there is forest on the tile the tooltip shows you need Animal Husbandry before you can clear it. That being the tech that gives that ability. Now, although polders come much later than these techs and are never going to be shown that tooltip, the underlying problem exists. The game has no code that says "hey you must first clear this plot before building that", thus you can build them on top of these features.
As always, I plead ignorance if these assumptions are incorrect.