I'm not sure if there is an option for this but I can't find it.
Basically this is what I want to do:
I have multiple files inside the folder and each file is not bigger than my upper limit for compression, however folder exceeds this value and all files get compressed in a single archive.
Can I disable this and only compress files inside the folder which are bigger than allowed limit?

No, there is no such option.

The whole folder size is checked.

The only way to disable this is to disable the compression or to increase the limit size.

If you really need per file basis, the only way to do it would be to process single files (not whole folder) -> later you can select all needed posts -> right click -> "Merge".

Hm... bit this is kinda important feature for series. For example clicknupload has 3gb upload limit. If you have series with 30 episodes in one season and each is lets say 1-2gb entire folder will be packed in one 30 to 60gb archive. If user needs just a few episodes they still need to download everything in order to upack it.
I guess hot fix is to disable compression but then I might have in same batch some HD series with each file exceeding 3gb.
In this case I wont have set of links for that host if I disable compression.

Will take a look more.

Edit:

As mentioned: If you really need per file basis, the only way to do it would be to process single files (not whole folder) -> later you can select all needed posts -> right click -> "Merge".

That's the correct way. Other way would be just too confusing and almost not possible to implement because of tons of settings for each specific host.