Where does the file owner on Windows matter, seeing that there are ACLs?

First of all, Linux does have ACLs – POSIX ACLs, which allow setting the permission bits for any number of users and groups. (Patches for RichACL, ACLs very similar to NFSv4 and WinNT, have been submitted repeatedly, but not merged yet.)

Ownership can be used as a sort of safety escape – the owner can always change the object's ACLs, even if the change would be denied otherwise, for example, if someone accidentally removed all ACL entries or denied all changes to everyone. (On Linux only the owner or superuser can change a file's ACLs, since there is no separate "change ACLs" permission.)

Another use of file ownership, on both Windows NT and Linux, is for determining whose quota should the file be counted on, if disk quotas are in use.

There is a big difference if you look at it from an administrator's perspective.

On Linux root can do everything directly - the account as implicitly all permissions on all objects in the file-system and beyond.

On Windows an administrator does not have permissions to do everything by default - only if you are owner of the object (file, folder registry entry,...) you want to change.

Take for example a folder an administrator needs to change the file permissions. If the admin doesn't have the permission to change the security settings of the folder he needs to take over ownership of the folder before being able to access/change it.

Update:

This feature is important because in an ACL controlled environment there may be the case that a file has an empty ACL which means that no-one has access (default deny principle). In such a case taking over ownership is the only way to get access or to delete the file.

The object owner always can change the ACLs.