I hope I didn't come across as being just a pedant, but it truly is an important distinction.
For a Certificated aircraft, or engine, there is a recognised procedure for repairs / modifications - it is called 'Compliance' with the original Type Certificate OR an accepted ( by the NAA, in our case, CASA) issue of a Supplementary Type Certificate. It can be done by (in our local case) a Part 21M engineer (used to be CAR35) and must be approved by the NAA. Once approved, it keeps the aircraft eligible for all original operational limitations.
For a Certified aircraft (or engine), it is entirely the manufacturer's responsibility to accept (or reject) the modification / repair scheme.
Given that the legal liability for accepting any modification/repair for a Certified aircraft rests with the manufacturer, it is understandable that the manufacturer may not be prepared to take on the liability of a third-party-designed change. Some LSA manufacturers are very helpful in this regard - Tecnam is one - while others are simply 'not interested'...
Let's talk actual examples. Modifying a C206 ( I think I have the right aircraft here.. not very conversant with the later Cessna models) for a 'jump door' could be done - since it is a Certificated aircraft - by (in this case) a CAR 35 engineer-designed mod. IF the 206 had been a 'Certified' aircraft, it would have required Cessna to approve the mod.
(To lighten up the conversation here, I can recount an example of which I am familiar. A family member had designed a freight container for use by the aircraft that bought King Island cheeses to the mainland; CASA was dragging their feet on approving it. Said family member sent them an email, pointing out that further delays would mean no King Island Double-Brie would be delivered to the mainland if this wasn't approved; cue instant action from CASA. Do you reckon Textron would have given excrement for THAT argument??)
In regard to spares for 2200J engines - it's a very vexed issue ( and since I have a 2200J but with many CAMit parts in it, it's of particular interest to me). My engine can only be used in either a VH-Experimental classified aircraft or a 19-reg aircraft, and the level of changes I have made to my own originally VH-reg ( it was ST1-00001, with a 1600 engine!), then changed to 55-reg, will make this an 'interesting' exercise when it's ready to fly (getting there..)
CAMit parts would have kept 2200J engines flying; I suspect that now, the only likely source will be Jabiru SA for barrels, heads and crankcases. I don't know what parts from the Jab. Gen 4 engine fit, but - without having ever seen a Gen 4 engine - I cannot envisage that the new barrels and heads will fit on a 2200J crankcase, as the through-bolts cannot - I think - be in the same location as for the 2200 Gen.1-3 engines. Happy to be further advised.