Copying from an ExFAT drive to Mac drive

NTFS supports both hard links and symlinks just like HFS+ (in fact NTFS supported these long before HFS+ was invented): en.wikipedia.org/wiki/Comparison_of_file_systems

exFAT does not, which raises the question what would apps do (like FCP X) which use those specific features? This is an exception to the general rule that the filesystem API is always the same -- there are a few corners where file system-specific features exist.

It is up to the application developer. The choices include throwing an error and letting the user take action, or adding additional application-layer code to handle what the file system lacks. A common way is creating "sidecar" files in the folder which contain the data normally kept in the resource fork for HFS+. Besides those additional sidecar files, the application must itself contain the code for handling that vs the file system. This is a hassle so developers must carefully choose which feature to implement.

However it's a good additional reason to use HFS+ where possible. In general you assume file system code is better tested and more reliable than application-layer code.

I'll need to test OS X (BSD) created soft/hard links on an NTFS drive someday, again. I know some years ago trying to integrate a system when I used to do that for a living, we had issues. Things may have changed.

My, my how this thread has grown and changed!
So for my wooden nickels worth; ExFAT is an okay format for mixed environments, but has some real limitations.

First it is a Microsoft proprietary format that is leased by Apple. Some of Apple's implementation is limited. Apple does not support ExFAT for Time Machine, Time Capsule, Airport Express, and unless I'm mistaken, no software RAID.
Also CCC, SuperDuper, do not support ExFAT for cloning or backups. I'm sure other apps too.
ExFAT is not journaled, so it is slightly more susceptible to data loss. This can occur if drive not dismounted properly, loss of power, computer going to sleep, etc… Recovery/restore can be tough.
NTFS and HFS+ are both journaled formats.

The permissions, ACLs, are different and limited under ExFAT, so when used in an environment that needs to limit user access to files, like a school, you are SOL. Apple's Unix underpinnings are quite robust by comparison.
As the OP found out, permission differences can be an issue, even in simple copying.
AFAIK ExFAT does not support resource forks so this can be somewhat problematic.
I think 32bit vs 64bit rears it's ugly little head and bites one where it hurts.
Linux support of ExFAT sucks with huge performance hit.

Having said all this, ExFAT is a big improvement over FAT32 in terms of file sizes. Macs and PCs can share files. It bridges both FAT32 and NTFS on the Windows side and Macs can write to it natively. You need a 3rd party program to write to NTFS like Paragon for Mac.
Black Majic now supports ExFAT along with other cameras. This is important for large video files.
I think most of the earlier formatting problems in Disk Utility for ExFAT are gone now??

Still if given the choice between MacJournaled HFS+ vs ExFAT, I would definitely go HFS+ and avoid having to troubleshoot an extra layer of format wars.
If I absolutely had to deal in very mixed environments with lots of older Window PCs (XP and newer), then it might prove better than NTFS (or maybe not).
If using ExFAT, just don't bump that external drive while writing files. Maybe get comfortable with Terminal.

Hope this helps, Greg