Not really sure where the confusion lies. Hasn't KTM essentially run this way, successfully for years? Coma and Despres were KTM riders but had their own dedicated staff, structure, and branding within KTM and the two did not cross over too much during the rally. As I understand, HRC will run in a very similar fashion. All 5 riders will be team mates but both sides will have their dedicated structures, one of which has been, in a sense, contracted to Speedbrain.
Did Honda essentially remove Speedbrain as competitors? Perhaps, but Speedbrain have proven themselves capable of producing a winning bike and a winning structure so I see it as Honda finally admitting to themselves that perhaps it's better to acquire experience rather than trying to accumulate it all internally.
Now I'm sure big money changed hands, so why a deal could not be made with Cyril is unknown as I certainly don't expect that Yamaha produced a better deal. Perhaps the ASO has kicked in a chunk as they realize that their package is better when Cyril is included than without him. I don't know.
One of the long standing rumors is that Cyril will be expected to win wherever he goes and if he doesn't, it highlights deficiencies in the equipment. I have heard from several high sources that HRC was a little gun shy of not being able to give Cyril a winning bike. If any of the new HRC riders don't win it doesn't necessarily point to the bike as the fault. If Cyril doesn't win, it may. It's a plausible theory, but fundamentally, I cannot wrap my head around a team shying away from the best talent available in order to shield a potentially inferior platform.