... Smoothing the floors over or building constructed floors that will get muddied will not block the growth of trees(And towercaps)
That is, for towercaps, regular trees will never grow on anything other then soil, so constructed floors will block those just as much as a road.(At least in their regular unmuddied state, I do not know for sure what happens to muddy outdoor constructed floor)
I have lots of towercap farms in my current fort with walking paths made of rough constructed floors and I have never seen anything sprout on these paths---even ones that have been muddy and untouched by dwarves for several seasons---so I think you're wrong there. (I have heard, though, that muddy constructed floors can have productive plots built on them.) I agree, however, that muddy smoothed floors don't stop anything; I've had masterwork engravings destroyed by towercap saplings sprouting up.
On a mostly unrelated note, I have
never seen a towercap reach maturity on a tile on which a stone was sitting. I've seen caps and shrubs sprout, but even after many seasons the caps never mature and often reach maturity
instantly after stone is removed from the tile. So it seems that forbidden items on a tile can prevent it from being blocked from walking by a mature towercap---not that it's very useful.