Is it ok to view Time Machine backup directly and store files inside backup.backupd?
It's perfectly reasonable to manually navigate your Time Machine backup with Finder, even though you would usually use the Time Machine app instead of Finder. Whilst it's not something to rely on, Finder will prevent you from making changes to a Time Machine backup.

I'd avoid storing your own files in Backups.backupd — put your own files outside this folder, there's no need to put your own files within the backups directory.