I know you are hesitant to go the route because of the extra expense with the FC controllers, but the way the Fractal gear works together as an integrated system can't be understated. And if you are only using one additional FC, all you need to connect the two devices is a single XLR cable. If you keep them close to each other you can easily get away with a 3 foot-er.
I approach cover gigs a different way than you do though. Neither way is wrong, they are just different approaches. I originally used a preset per song approach back in the Axe FX II days but as you know, setlists and song order can be very fluid in a cover band situation. There were a few too many instances of me hunting for the preset and coming in a bar or two late for my comfort so I switched it up to using 3 basic presets (clean/crunchy/heavy) that gave me an easy 'base' sound and then effects were switched in and out on the base for individual songs situations. I use scenes heavily for switching in and out of lead tones or stunt sounds quickly.
It gets pretty quick to switch in and out sounds for different songs when you are only using 3 presets and 3-4 scenes per preset. It also lets muscle memory kick in when you use a system for each of the presets like - scene 1 base (typically clean to eob) sound, scene 2 like 1 but with added balls, scene 3 effects, scene 4 lead. Combine that with channels on the effects and you can string together radically different tones with a minimum of dancing. For songs that required extra effects or stunt sounds, I'll throw that in as an extra preset. For example, I set up an intro for a song using M@'s Blade Runner preset that went over very well.) But most shows, I got by with 3 or less presets typically using 2-4 scenes per preset. That said we played mostly pop songs not prog epics.
I guess that TLDR of the above ramble is:
Don't fear using an FC-6 or FC-12 with your FM-9. It just works and the extra setup time for the second bit of kit is really negligible due to the simple one cable plug and done method Fractal has implemented. If you absolutely need the switches, it's the best solution. Otherwise you need to do some dancing or change your methodology.
The thing I worry about for you is if you get an FC-6 and suddenly you add a song to your setlist and need a 16th switch...