I see no reason to change things now if you are going to be paying out of pocket, chances are things will work ok until something breaks, just expect to have that extra expense when it does. Think about it like having bought a car and finding out because someone put a bolt in from the wrong side the engine must be removed to change the alternator, turning the $450 alternator replacement into a $1,000+ job...
Ike
p.s. what is the pipe stub to nowhere?
p.p.s. When it does come time to replace whatever breaks, please don't let them cobble together mess like this, have them add a couple of $2 unions so equipment can be removed without cutting everything out.