Which to use depends on the kind of game you plan on making. The main issue with using Root Motion is it’s event driven where in-place is reactive to changes as driven by the movement component and is required for any game that is network compatible where it’s the capsule that is replicated.
If a network component is required things get technically more complicated as to tracking players in real time with in 3d space and since RM is event driven then you would have to replicate the event and like physics would be difficult to replicate the same requirements that the MC provides. You could trigger an RM event and not know where it’s going from client to client unless you make your own tracker.
Will the first workflow cause strange problems in the future?
The simple answer is yes you will have problems between coders and content creators as the movement component provides everything that the coder requires as far as creating the necessary game physics and movement with out having the necessary root motion as it’s the RM that moves the player and not the capsule of the movement component.
RM does produce the better result as far as a visual, and a good choice for single player games, but with out the movement component would limit you game to single player only.