I am in the process of setting my short bus the same way. Things I've noticed so far are with my bus being an HC bus, loading the bikes from the side takes less interior space but need a clear space next to me to unload. Unless sealed off, your bike fumes will be inside your living space and so will all the dirt n debris n liquids too. Being inside the bus is less likely to be tampered with or disappear. Being in the bus you wont have to worry about trailer speed limits either.
Trailers are nice to keep the dirt n debris, fumes,and liquids out of your bus. Will also give more space inside the bus for living. BUT, trailers get stolen and are easily to broken into. Not many people want to brake into a bus.
Good luck with your search and adventure.
2002 E450 Thomas/ U-JOINT 4X4 family hauler
1954 Crown 35 foot RV conversion
1945? City Bus (unknown manufacture) yard art
Plus more vintage coming...