Application-only authentication limits are applied on a per-app / ID basis, not per owner of the app. Note that app-only auth will only give you access to a limited number of read-only endpoints, whereas user auth will let apps post content etc as well.
This is not currently documented, but you are unlikely to have an issue unless you’re building a lot of bots. There’s a limit the creation of a small number of apps per day (this is also not documented as a specific limit, as it varies to prevent spammy usage of the platform). You should not use multiple apps / API keys to try to circumvent rate limits.
Modify/update would require a user context. In that sense, if one app posts content on behalf of a user, another app could come along and delete it, if it had been authenticated to that same user context.
