Multi-Domains is for sub domain installations only and will not work well for subdirectory install

I would like to use domain1.tld/shop and domain2.tld/shop to go to the same shop.

There is allot of confusion about subdirectory for multisite. Since there are no actual subdirectories why would the following statement in the usage section of Multi-Domains indicate a problem.

"Please note: Multi-Domains is for sub domain installations only and will not work well for subdirectory installations."

Please explain this statement and what the limits are. Thank you