Interesting that the front wouldn't fit....
In all likelihood it will be easy enough to adapt the old wheel with a set of custom axle and disc spacers? With the wide radial calipers more clearance is needed so probably the triples and hub are wider. I doubt the disc bolt pattern has changed, it's been the same on every 125cc+ KTM made in the last 20 years.
KTM even has a front disc spacer that could used, they put it on the LC4 SMs with the fat gold 4 piston Brembo caliper. 210mm width fork spacing on those bikes vs. 190mm for most other KTMs incl. 950/990.