It has very little to do with Boeing in this case. But blaming Boeing in the title gets you more clicks, and clicks equals money for journalism.
Boeing is not free of responsibility here, they chose to sell said engines as an option on their planes. They have worked together with Rolls Royce to integrate their engines with their plane. In theory, engine problems could even be caused by Boeing's software mismanaging the engines.
It is not rare for plane contracts and engine contracts to not be signed simultaneously: the engine maker might be decided months after the contract for the 787 is firmed. Aircraft engines do not qualify as "some 3rd party component".
A slightly better comparison (but not perfect) would be if you buy a server from Dell with an Intel microprocessor, and there's an issue with that Intel chip: will you blame Intel or Dell? After all you could have picked a Dell server with an AMD processor.
The engines are also mounted to the air-frame at Boeing's facilities (since the plane can't really leave under its own power until that happens), so whether the airline pays Boeing or R-R for the engine is just an administrative detail.
As for the server comparison, if you buy a Dell computer, your warranty is from Dell. If something needs to be fixed, Dell will do it and then argue with Intel about who foots the final bill.
The airplane world is a lot more complex, and that is exactly my point – the blame is not 100% with R-R and 0% with Boeing – or vice versa. There's plenty of blame to go around.
The contract is signed directly between the airline and the engine maker. Of course the engines are installed by the OEM (Boeing, Airbus, etc.), as otherwise delivering the plane would be problematic to say the least...
EDIT: another, more relevant example: Norwegian ordered 19 Boeing 787-9 in October 2015, and selected Rolls-Royce to power them in February 2016 (https://atwonline.com/engines/norwegian-selects-rolls-royce-...)
So airlines sign big contracts with engine manufacturers for new engines, parts, supplies, training, etc.
This also happens even with small single engine airplanes, those engines need overhauls every so many thousand hours, so one option is to trade in your old engine for a refurbished one instead of overhauling and keeping the same engine. For some larger fleets companies have contracts with engineer manufacturers or service centers for this.
Airplane parts are intertwined believe it or not, their engineers spend years working together.
May as well start 26 shell companies named BoeingA to BoeingZ and pretend it was all someone else's fault.