alternative to android build in encryption?
You already indicated the possible use of an app. And indeed, next to the so-called "vault apps", there are several options for Encryption of Files and Folders which work transparently on the file system. For some, you still will need to use "specific folders" which you encrypt, though – while most of the others fall into the category of requiring root access.

Some example apps you might wish to take a closer look at include, but are not limited to:


Cryptonite (based on EncFS)
EDS (uses TrueCrypt containers)