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The heat from brazing causes the tubes to expand and contract and as the heat is focused on one side at a time, this has the effect of pulling the tube one way, out of line.
Apparently, since the jig holds it all together, the tube will pull but be held in place and when the fillets cool, you'll have built tensions into the frame which can cause cracking or failures in the future.
Don't think any framebuilders will braze a full frame in a jig, just tack as M_V says.(This is what I have read, I don't have enough experience to say either way)
Yes. I guess an alternative would be to split that section and have two pieces going up and down at ninety degrees (or more) from your central extrusion.