The patent covers *creating* filenames that don't match the 8.3 pattern. You can read them all you want. You can also delete them (one of the design criteria for VFAT was that old machines delete correctly, so it cannot possibly violate the patent).
Linux could make its own method of making "long filenames", probably a hidden file. It could read both the XFAT names and this new hidden file when listing and finding the files on the disk. If a new file was created that did not match the 8.3 pattern then it would create a new 8.3 standin name and add the name to the hidden file.
All FAT removable media would look fine on any Linux machine. But you put it into a Windows machine and suddenly some of the long filenames are wrong, truncated to an 8.3 version!
Just to cause Microsoft additional trouble, it should probably assume that any bytes are legal in the 8.3 names, thus lower-case letters and punctuation can go into them. This would screw up Windows machines reading the disk even more, certainly some ancient code in there is making assumptions that are not true.
These techniques have been used by Microsoft to attack competitors for decades, but it is possible they will work in reverse here.
PS: For the vast majority of users of cameras, etc, it won't make any difference. They only write 8.3 names. Where it will screw Microsoft up is if phones and things where users can name their files start doing this and start accepting standard removable media.