That's a real downer. You might just get away with it but at the risk of investing a lot of further effort only to find that the cylinder / boiler joint can't be well sealed. Also, a boiler inspector, assuming that he knew, might not be very keen on the departure from the published arrangement.
If you put in studs prior to mounting the cylinder, I think that you would find difficulty getting the studs through the cylinder flange unless you elongated the holes in the flange rather a lot and I don't see much real benefit.
My feeling is to consider drilling out the holes, say 6-7mm, countersink, and silver solder in 4 bronze bushes to be drilled and tapped. Not a too difficult job for someone who has boiler making expertise, and perhaps oxy-propane kit for localised heat. The bushes could be filed to blend with the boiler outer surface.
The existing threads need protection whilst soldering
Perhaps the local club has someone who can help. Best of luck.
clive
Edited By Clive Brown 1 on 25/08/2019 09:03:18