The answer will potentially vary depending on the airline involves, however in my experience of flying Business Class across multiple airlines on both paid and award/upgrade tickets I would say the experience is exactly the same.
My main experience is on United Airlines. In this case the perks you receive are exactly the same for all cases, and there is no distinction between the tickets. In the specific example you mention of meal selection, United prioritizes meal selection based on status, and this applies equally for award, upgrade and revenue passengers. I don't recall any other airlines stating that my meal selection would be affected by whether I was on an award/upgrade/paid ticket.
The only difference I can think of with United specifically is that many years ago they used to limit access to their Arrivals lounges to only "paid" business class passengers, however even in this case "paid" included both revenue and award passengers, just not passengers that had been upgraded to business class (even if they had 'paid' for that upgrade). They changed this policy many years ago to allow access for all business class passengers, including upgraded tickets - and have since removed all of these lounges anyway so it's no longer relevant.
I've also flown award/upgraded business class on multiple other airlines (Singapore, Thai, Eva, Air China, Qantas, Virgin Australia, ANA, Turkish, Lufthansa, American and Swiss to name a few that spring to mind) and I don't recall having any perks limited based on being on an award/upgraded ticket.
Specifically for upgrades there can be differences based on when the upgrade occurs. For example, if you are upgraded at the gate then you likely won't be able to make use of any additional free checked bags, priority security, and probably not even lounge access as by the time you are upgraded it may be too late to access the lounge. For airlines that allow ordering a specific meal in advance, obviously this won't be available if you are upgraded shortly before boarding the flight.
Many airlines do apply different rules for "non-revenue" passengers, however this term does not refer to award/upgrade passengers, but instead to people like airline staff travelling on 'free' (or more normally, very highly discounted) tickets. In this case it's very common for things like lounge access to be specifically denied, and meal selection could certainly be impacted (eg, non-rev passengers are given lowest priority for meal selection on United Airlines)