I don't think either of those setups is more right than the other IMO. Ask them why they think your current setup won't work - if they cannot give you a solid answer then I'd say they're simply going with past experience out of habit.
Try this - which of the two setups has fewer fittings? The more fittings you use the more flow you choke off. 90s in particular are bad, Ys might also not be real good but some fuel companies make some good ones - pricey though.
So long as both sides of the rail get fuel it ought to be fine I think. Some have input duel on one end and the middle too but I'm not sure that's as good. However I'm not sure I can exactly say why that might not be good so.....
Heh, any engineers on the board who could figure this out? It's a flow problem

Only issue I might see with dual lines aside from cost is the wall friction being higher - but enough to make a difference?
