What are the additional things that are being added? I thought things like Battletoads appearing in Shovel Knight were what we were talking about. The way it's being spoken about here it sounds like it's something much more significant. I'm not a developer but I'd assume that adding an extra character wouldn't represent a lot of extra work when doing the port? Are Xbox One versions of games getting additional levels or gameplay features added to them? Genuine Question, I'm not aware of any other differences other than Shovel Knight's extra character(s).
Adding an 'extra character' can be a huge amount of work- the new characters in Sony/MS's versions of Shovel Knight involve new stages and items that then need to be tested against everything else in the game. Dropping new elements in without considering everything it may or may not have to interact with could be disastrous, you are looking at dozens (maybe even hundreds) of hours of work and thousands of dollars depending on the process used.
Not only that, but at this point I think the success and critical acclaim surrounding Shovel Knight makes it something of an outlier- they had a hugely successful (and well run) kickstarter and PR campaign, followed by widespread press coverage. I think it's fair to say YCG, despite the financial hardships of indie development, are probably going to be OK for at least a year or so on the back of it's success. Not every team scores a huge hit on their first outing, after months of spending their own savings, it takes a while to pay off the dev costs, it's not a case that every indie team is suddenly rolling in cash because their game is up on the PSN store/steam. They are starting at a severe loss and putting faith in a game taking off or at least being successful enough to keep food on the table, any argument that bases what is reasonable on the assumption that all parties are equal in a negotiation isn't very fair when their MS contact probably isn't betting his savings, months/years of work and career over the project being a success.
It costs nothing to allow devs to publish their finished game, asking them, with no knowledge of their financial situation, to commit to even a months unpaid work is ridiculous when MS are unlikely to send a group of their own devs to work for free. A months salary is a lot for a small company, and even more for a small company that might not have paid anyone for months during development.