REgarding minor mods, here's what Part 21 says:
21A.95 Minor changes
Minor changes in a type design shall be classified and approved either:
(a) By the Agency; or
(b) By an appropriately approved design organisation under a procedure agreed with the Agency.
I sent email to EASA and they replied saying that you apply to them (Form 32) and then they delegate the NAA to take charge of the analysis of mod. Then they receive the OK from NAA and gives the approval.
cheers
M.