I would say yes,swapping the lines might cause trouble---.
I put a master cyl. I had from a truck I scrapped that was a recent rebuilt one I stashed away in my shed ,still attached to the vacuum booster,full of fluid...
My '82 K2500 needed a master cylinder,its original was oozing fluid from the rear of it,causing the rear chamber to go dry eventually..being cheap and unemployed,I decided to use that "spare" one--my truck is a diesel,with Hydraboost though,but the master's both had the same bolt pattern and depth where the push rod goes---the original master was "square" and had a smaller resivour in the frint than the rear,while the other had an oval shape and 2 equal sized chambers for the fluid..
For my lines to fit,I had to swap the one that used to be up front,to the rear hole,and the one that went to the rear,up front...after bleeding the brakes and going for a ride,I found the right rear wheel locked up VERY easily,and the first time I drove it,I had the misfortune of having a cop directing traffic step right in front of me and put his hand up ,and I was going 35+ mph,he must have thought he was superman--I tried hard not to skid,but just the weight of my boot on the pedal caused the RR wheel to skid,and the truck barely even slowed--this resulted in a butt reaming from the cop,and I was lucky I didn't hit him,or get arrested--.
Anyway,I have not determined yet if its due to the master cylinder lines being "reversed" thats causing this,or if its just the rear shoes,which were soaked with gear oil & brake fluid previously,(that I washed off thoroughly with brakleener) that might be causing the "grabby" rear brakes,I didn't have the cash to replace them,and they are like new as far as lining depth...
I was going to buy two brake line adapters so I could swap the lines back where they were on the original cylinder,but this master is weeping fluid now too,so I might as well go buy another rebuilt that matches up to my original,because those adapters will not cost much less!...I have noticed those adapters sometimes come with a rebuilt master cylinder,and the master dont always look the same as the old one though!...so I cant say for sure if reversing the lines causes trouble,but seeing one line goes to DRUMS in the rear and DISCS up front,I'd say it does matter....