Whilst the boys should have won if they had sold better, even by a tiny amount, there is a justice in the girls winning.
Whilst the boys had the better return on investment by far, they would not have got much repeat business if this had gone on for long in real life. The low quality would mean lowering the retail price and so profit falls. You can only go on for so long selling over priced junk. Also virtually no chance of selling to trade without a massive price drop, which they wouldn't be able to go down to.
The girls' lower ROI doesn't really count (except to some investors) as the gross profit is the same. Same size teams, same wages bill, same equipment costs, etc. In time they could make a higher profit margin by sourcing better and changing the recipes. If they can convert a chef to buy (cos he wanted to be on tv maybe?) they should have little trouble building trade sales.
Typically for The Apprentice, these handmade products are sold for ridiculously high prices. As a guide, Waitrose sell six organic bangers (400g) for £2.39. Their dearest are just over £3. Faced with customers who have some idea of prices, both teams should have made a loss. Although the girls are in a better position to lower their costs, though not in a one day task without losing. In real life, yes.
Neither team seem to work out their costs until they had committed themselves and were half way through production. That's probably down to the tight shedule. So there is an element of luck there. The girls were better organised and put two on the task, just as well as theirs was the riskier strategy.
It really came down to selling. Both lots were too pricy, but at least the girls' were more likely to convert a taste into a sale (once they got their act together). The boys struggled to find enough mugs at the market, and then their act fell apart by having no idea who might buy these things and so half of them almost stopped selling. It's the tortoise and the hare. The hare should win but doesn't if it stops concentrating on what it's supposed to be doing.