Disadvantages of multi-store using multiple directories?

I want to use the multi-store feature with multiple directories instead of using subdomains or whole other domains. I got it working just fine using with the apache alias feature but wanted to see if anyone has run into any problems with this since OC clearly states:

Don't use directories to create a new store. You should always point another domain or sub domain to your hosting.

The problem is SEO

http://www.mysite.com/mens-hats may be a link in the first store
or "mens-hats" may be a subdirectory. The SEO will override that and you will get an error in your main store saying it cannot find a category or product page called "mens-hats".

That is why it must be subdomain

I guess I should have given a better break down.

Store 1: http://www.my.com/mens-cloths/
Server Install Path: /var/www/my.com/httpdocs/mens-cloths/

Store 2: http://www.my.com/store2/
Apache Alias: /var/www/my.com/httpdocs/mens-cloths/

In this situation you don't have any conflicting SEO as far as I can tell because even if you did duplicate a category with the same name as the folder it would act as a subdirectory due to the alias. So for instance in store 2:

http://www.my.com/store2/mens-cloths/
would return via alias as:
/var/www/my.com/httpdocs/mens-cloths/mens-cloths/

This is also assuming that opencart is not installed in the root directory but a sub folder.

Also want to note, that I did successfully get this working simply using apache alias. I just wanted to get some feedback to potential problems I may encounter while I am developing this site.