There isn't going to be a very simple solution to this, the corn-cob style roughing cutters that the machine typically uses are really geared toward steel. The design of the cutting surface grind is attributed to steel. When it comes to aluminum there are soo many factors that will affect the burr, on tube especially. I dealt with this problem years ago when the Iron works I worked at had a railing job come across that required Al tube. It came down to having to get a very specific alloy in a strict temper to be able to notch it and bend it without issues.
This may be a lot of trial and error on your part to find a cutter that works, which sucks considering how expensive those damn cutters are. Those cutters are not proprietary to the machine, however, those machines are typically the only machines that use the roughing cutters in a 1" or 1-1/4" shank diameter in 6" length of cut. I would suggest reaching out to the cutting tool companies to see if they have any suggestions. You can try changing the pitch of the cutting edge, the number of cutting edges, the grind of the tool etc. A brand new super sharp cutter should reduce the burr also, those roughers are great at just mauling their way through but not so much for delicate work, the cutter you move to may wind up being an uninterrupted style of tooth.
Have you talked to Mittler about it to see if they have any suggestions? One suggestion, and I know it sounds off kilter here, clean the tube for welding before you notch it. Notch it, leave the burr on there and just weld over it. As long as you use a solvent of some kind in between the cutting procedure and welding to remove any oils or cutting fluids from notching the burr would just get consumed in the weld puddle.
One last option, worst case scenario, if the quantity of work is there you can always outsource the notching to have the cope/notch laser cut. Best of luck with this one.