How important is it...

There's tons of kayaks out there with clean decks.  the main issue with most is probably the foot pegs.  I would pick one with integrated geartrack probably, as that keeps decks relatively clean, and gives you options for accessories that can be added and removed pretty easily.

I think with raised seats that the width doesn't really matter as much, since you really don't need to straddle your kayak, and you're already in a higher seated position. 

There's a few upcoming models that I know of that will have clean decks from Native like the Slayer XC.  Might be good to wait until Demo season to try one out in person.  I wouldn't have an issue with someone bringing a fly rod with them to one of the demos that we hold, and I'm sure some of the other manufacturers would be fine with them as well.  If there's a specific model you're looking into, ask the shop to have it available for demo for you.

One of the reasons that the Mayfly has a wider deck is that it has a shallower water profile and less keel.  If you were to build a kayak with a similar hull shape but make it narrower, it might be fairly unstable for folks from a primary stability standpoint, and secondary would be lost without a keel.  Would also result in less overall weight capacity due to lack of volume.

Boats like the Mayfly are purpose built for midwest/northeast river fly fishermen, who need kayaks with relatively shallow drafts and higher maneuverability in rivers.  we don't do a lot of shallow draft river fishing up here in NorCal like they do there with the river bassing series.  Just different strokes for different folks.

They're designed for flat, calm bayou fishing and maybe the flats where the current kayak fishing boom seems to be driving the market.  I wouldn't have given them a second glance when I lived in the Midwest.  Just MHO.