So everything is relative (hoho pun intended) when it comes to security.
The reasoning to disable relative paths in standard mode is that it allows you to walk up/backwards in the folder chain. This was never a issue with QV as you could not create on the server however with QS users now have the possibility to develop on the server so you don't want to expose the entire file system to the user.
You can still though have a root folder in standard mode which you walk downwards in.
Let's say you have a folder connection named Data set up to C:\Data\ then you could still walk downwards,
Load ... FROM [lib://Data/SubFolder/MoreSubFolders/Datafile.qvd]
This would allow you to still have a single entry point into a structure of data BUT this also only give one opportunity to define security rules for that connection. If you are expecting a lot of different users that have different data access needs then a folder connector per role is a more scalable approach