Would this raise your hackles as a DM? They are not allowed together on a technicality, but really it shouldn't matter from what I can tell.
The flowing monk replaces your 2nd monk bonus feat with unbalancing counter. That overlaps with MoMS's change to the bonus feat options. MoMS doesn't actually replace the 2nd level bonus feat, it just changes what feats you can choose from.
Seems like a waste of an awesome duo for a technicality. What would this break that I'm not seeing?
The only thing it breaks is the rules.
in a home game I personally would say ok.
However it does open the door for a lot of other archtype combos that should work for the same reason but currently do not.
Such as...?
I'm currently Foghammer's GM, and I don't see this as an issue, but if anyone does, I'd like to know. I don't want to allow something broken, but I just don't see this combo being too powerful.