SEGA is not a charity and will most likely not give the rights to Yu Suzuki for free.
In a recent interview, Yu Suzuki was asked directly if SEGA will get any money for the licence. Yu said that he can't comment on that.
It's pretty obvious that SEGA does get a cut, otherwise there would not be a reason to be silent about it.
Does SEGA get money from the Kickstarter? - Probably.
Yu always mentiones that Sony and Shibuya Productions won't get a cent from the KS - but he never mentions Sega. Futhermore he always says that "more" money from the KS can be used for developement, not "all" the money.
Obviously he can't talk about SEGA's involvement, but you can easily sum one and one together.