In Do layovers count in the 90-in-180 Schengen rule?, we (apparently) concluded that changing planes doesn't risk exceeding ninety days. What about a 46-hour bus ride from Romania to U.K.? Possible, but extremely uncomfortable to not get off the bus for 46 hours.
Yes. It counts. You will enter the Schengen area as part of this trip.
Under the right circumstances, you can make certain international-to-international air connections without entering Schengen, as airport transit lounges are secured areas that may permit you to get to your next flight without going through immigration.
That is not how buses work. The bus driver is not an immigration officer with the authority to confine you to the bus. He doesn't stand at the bus door and stamp you in and out of Schengen as if the bus was some kind of supranational zone. You will be inside the Schengen area with the ability to get off the bus and go anywhere. You get 90 out of 180 days inside Schengen. The fact that you choose to spend several days of your 90 days riding a bus across Europe instead of touring a city doesn't change anything.
Yes, it counts, there are no exceptions for layover, transit or anything like that. If you cross an external border (which a bus must obviously do), you have to undergo a full border check and will get an entry stamp. The only reason it is sometimes (but only sometimes) possible to transit without a visa and/or without using up time from your 90 days is that European airports often allow going from one plane to another without going through the border checkpoint.
With bus travel you enter the country.
I have never heard of buses that make it impossible to leave the bus for a travel of more than a few hours at most and non that crosses whole European countries that allow for foreigners without visa.
So your time in the Schengen zone counts against your 90/180 days.
Changing planes within the Schengen zone only does not count if you stay in the international zone of the airport, two changes within the zone means you enter the zone and any time there will be calculated against your 90/180 days.