18" rear wheels for MX?

You'll be fine.  They went to a 19" as it has less roll over in the corners for side loading.  Not sure us mere mortals can tell the difference.  The 18" extra sidewall gives better flex and traction for woods riding.  At 50+ (A-woods, B-moto) I don't notice the difference and just like the feel of the 18" over the 19".  The hardest part is finding a suspension setup that crosses over well.  

I'm an A motocross racer and I really don't like the 18" rear. Granted, I had a 140 Euro tire with a mousse in mine. It made the rear of the bike feel like an anchor over the jumps.

FWIW, especially on a KTM, I would buy a spare 19" wheel to swap for moto. KTM wheels are very interchangeable throughout their year-span. 

The 18" rear works just fine for MX as long as you use a MX specific tire. I raced with one for a whole year on one of my 350's. The biggest issue with trying to use FX for moto will be getting the suspension set up, as pointed out above, and getting the right gearing. One of my riding buddies raced MX on a Factory Edition KTM 350 XC-F and we had to try a couple different gearing ratios to work around the different transmission. 

I ran an 18” pretty much exclusively on my 450. I loved it. I switched back to the 19” a few times and ended up preferring the 18”. They’re easier to mount and I feel like I had better traction. I’m VET B level rider in Southern California and cannot lean the bike over enough in turns to really notice a difference. The biggest difference in feel I had was running fresh tires. When my tires were fresh, like 2hrs, I felt like I could really corner well. 

One thing I’ve noticed at local tracks are the pro and expert level off-road riders riding MX. They’re on 18” wheel with large fuel tanks absolutely ripping!  They often appear to be the fastest guys on any given day. Their corner speed and ability to absolutely lay down some of the biggest scrubs I’ve seen lead me to believe that the 18” will work just fine for me. Haha. 

Anyone who says they can't ride moto with an 18 inch rear shouldn't be giving out advice. You'll be fine, I've ridden 18 inch rears since 2009, the cross-country models are really the bike most people should be buying.

When I switched from 18 to 19 on my YZ250, I noticed the rear end sitting higher with the bigger wheel and the bike cornered better. I would consider sag adjustment (fork angle geo) with different diameter wheels.

The 19 will flat much more easily in Rocky woods.

I’ve ran both, 18” is better for me. The only downside I’ve found is with a tall, soft sidewall tire (Pirelli in my case) lower pressure made for some sketchy jumps, the sidewall was collapsing on the take off and I didn’t know what direction I was headed, jumped right off the track a couple of times. 2 psi more and it was mostly fixed. 

18” AT82s work great.

18" wheel is supposed to be the same OD but most of the time, it's a little shorter/smaller after installing the tire. This difference effects the final gearing.  

Husqvarna (and KTM) publish the gear ratios for the FC and FX. You'll see they're not identical, but every time I've ridden the 6-speed I always enjoy the 1-5 and the 6th speed is just the cherry on top. 

What I've seen over the years is that the 19" wheel is more about making the bikes better for Supercross rather than better at motocross. I don't know if the production rule requires wheel diameters be the same as stock at the top level. Local tracks obviously don't care.