The best way would be:
Buy a new transition strip and have it go all the way across.
Cut a return and glue it to the end of the lighter quarter round.
Make a return for the darker quarter round and ...
Oddly, I’d caulk between the window frame and the filler and spackle the wood to wood joint.
The caulk at the window frame will have a little bit of give with dissimilar materials.
The spackle at the ...