Recursive blueprints should honor any filters that the deconstruction planner has in it if it's loaded with one. Right now, this would be a pain as you'd have to extract the filtered entities and scan for them in the deconstruction area. But in 0.18 there should be a new parameter that lets you apply a filter in the deconstruct call, and it should let you just pull the filter out of the decon planner and feed it in.

The tricky part is that deconstruction planner is used as a command signal. Using it like a blueprint would require a new deconstruction command and break old saves.

Aren't chest contents and the signal treated differently? When you got the deconstruction signal, you could check to see if the recursive blueprints chest also contained a deconstruction planner. Also, I think deconstruction planners can be in blueprint books. So if the 'build' signal specified that a deconstruction planner be built, the filter behavior would be activated instead.

The reason I wanted this, is that I was trying to build a glider that didn't destroy trees unnecessarily when it picked up the previous location of the glider.

Just FYI the mod conman does provide a method to do a filtered deconstruction with filters set by the circuit Network. It does use absolute coordinates in X,Y and not relative to the Position of the machine, but with the "Location combinator" mod, it is quite easy to adjust those coordinates.
It also uses bounding boxes, where you give the coordinates of two Corners of your rectangle instead of Center+ size. So you Need to adjust the coordinates a Little more