Simple answer: No.
The same is true for any data structure. If you don't understand the data structure you can't find anything in it.
For data recovery purposes there are tools which will scan data (a drive) and search for signatures it understands (eg the start of a jpeg file). One example tool is photorec
This technique lets the software find some files without understanding the file system. But it's messy and unreliable. This technique can't handle fragmentation well and only works for some file types. It can often result in corrupted files.
There are cloning tools which are file system specific. For example if you know the partition type is ext2/3/4 you can use a tool like e2image to copy files across without using the Kernel's file system driver.
You could also resize the file system before cloning with clonezilla. Eg: use resize2fs to shrink the file system first.
Beyond that, your only real option is to mount the file system and copy the files across with
Regarding CloneZilla's decision not to implement resizing: Filesystems are generally very complex. There are some simpler ones but ext2/3/4, reiserfs, etc. are't the simple ones.
It can be simple to parse enough information from a file system to determine which blocks it's using. Some file systems even have a nice neat table just marking which bocks are used / not used. Parsing this would not require knowledge of files at all.
As an example, ext3 by default uses blocks of 4096 bytes and block groups of 32,768 blocks. Each 128MiB block group contains a "Data Block Bitmap" showing which blocks in the group are in-use (see reference). So without knowing anything about the files themselves, a program can parse just which blocks are in-use.
However resizing a file system requires a much more robust knowledge. Without knowing specifics of ext2 etc, possible snags include
- failing to update cross reference pointers or pointers to / from meta data
- failing to update checksums
- failing to update block usage bitmaps correctly
It would be very easy for a naive developer to implement a resize in a way that corrupts the file system or destroys meta data.