Ducati currently puts three 2018 bikes on the grid (third one going to Petrucci), HRC puts 4 bikes (Cal and Nakagami both on 2018 bikes).
The way I see this unfold is MarcVDS getting one 2018 and one 2019 bike next year (With the 2019 bike going to Zarco if they manage to sign him, Luthi is on a 1 year contract IIRC). And then perhaps in 2021/22, VR46 gets two further bikes (Current or year old, we will have to see).
Another reason why Yamaha might push to get MarcVDS signed is that it will get Morbidelli away from HRC and into the Yamaha-Rossi constellation.
I thought Honda only had 3 full factory bikes with Nakagimi on the same deal (customer bike) as MarcVDS?