I would expect three year old injectors to be in very good shape. One being bad is rare at that young age. I would just replace the one, unless something else suggested a greater need(injector recall or the vehicle not being driven for a year or more at a time). On older vehicles with long storage times, any rough running may end up being injectors, on those I'd replace all at once.
The secondary injectors of the new 2018+ Ford GDI's should greatly reduce the intake valve carbon build up. That was the sole reason for the new system, to inject fuel before the intake valves and keep them clean. So the dealer says there is/was carbon build up, did they say it was on the intake valves, or just on the other intake surfaces(intake itself) etc?
I would only worry about the intake valves, build up on those does eventually lead to the valves not seating properly, engine missing and poor running etc. The rest is just annoying from the PCV operation, not necessarily bad for the engine. Intake valve carbon build up requires removal of the heads to clean that out, and should have the valves removed and a new valve job done. I wonder how Ford has handled those head issues so far for the older(pre-2018) GDI engines?
I wouldn't mind a catch can, but I do not want one, they require constant maintenance. I would go to that as a last resort, after trying to improve the OEM baffling system in place(underside of valve covers typically).