Chris @ CJS can't flash the ecu, only hilltop, feck knows how he does it and others can't.
Are you sure? CJS told me that they do some KTM's and they (KTM) are listed on his web home page - but I think the list of individual bikes is way out of date. Best to call and ask I would say, rather than take the word of one tuner that none of his competitors can do what he can.
http://www.cjsracing.co.uk/
ECU Unleashed also list several KTM models on their site:
https://ecunleashed.com/product-category/motorcycles/ktm/
CJS does a lot of direct ECU programming and on my Yamaha Super Tenere Hilltop were unable to alter the Fly-By-Wire maps which is needed to remove the restrictions in the 1st 3 gears, CJS was able to do this and gave me the throttle maps I requested for Sport and Touring mode, they also fixed up the fuelling for a full Arrow system that ECU Unleashed charged me £400 to do and had failed at miserably.
Hilltop did a remap of my ZZR1400 and it was very good, but with that to remove the restrictions they threw away the secondary butterflies - but at the time nobody was altering the fly-by-wire for the ZZR, but this is now being done by a few tuners (including CJS) CJS can also remove top speed limiters and make other changes to the ECU (depending on bike)
I certainly do not want to get into what is the best tuner / dyno kind of debate as it is pointless, recommendations from happy punters is always good in my book, and I have been happy with CJS and Hilltop.
I also pay little attention to Dyno graph comparisons, a before and after on the same dyno on the day of the work is good, it can be rigged a little by the dyno operator, but I think most are honest.
My S10 went on 3 dyno's and I know it is pointless comparing between them, but on each one I could see the changes made and the effect they had - but this is only a small part of the story as it is a WOT run and most people spend relatively little time at WOT, the way the bike responds and feels on part throttle is far more important and this cannot be seen in a graph so owners comments are as good, if not better than dyno results in many cases.
As most bikes are not very well fuelled from the factory (as each bike is slightly different, plus they have to abide by emissions regulations) a custom remap by a competent tuner is always going to improve things to a noticeable degree, be it an ECU Flash, Power Commander or other device, some folk can do more (like ignition timing, map each cylinder individually and throttle maps) than others, but you pay your money and take your choice.
If I was going to have my bike re-mapped I would talk to Hilltop and CJS, look for other reports from punters (I think Hilltop have a good following for GS and now KTM) and then decide who I want to do the work.