This is not an ultimate deal breaker, but I'm wondering if there's a way around it.

Silverstripe creates navigation with a directory schema: domain.com/about-us/
Instead of: domain.com/aboutus.html

As a result, if I pop in the directory level destination to another server package (not silverstripe) I am getting a 404 error... unless I add the actual page.

domain.com/link/ = 404 error because link is a link database ... not part of SS, but a legitimate destination on the server.

domain.com/link/index.html = the link database.

Okay, normally, I'll tell people to go to yadayada.com/blog ... because I don't have to add index.html... the server will automatically bring up the page.

Plenty of websites have multiple programs and packages running on one server. I'm happy to have silverstripe manage content, but if the URL requested is out of its domain, silverstripe should not, ideally, be controlling the destination page.

Any idea how to disable that?

here's a one possibility how to do it for 'CRM' direcory and all it's subdirecotries.
First, move the line

RewriteEngine On

to be the first line in .htaccess, then add

## CRM is not in SilverStripe
RewriteRule ^CRM$ - [L]
RewriteRule ^CRM/.* - [L]

and finaly put lines after
### SILVERSTRIPE START ###
...

If you many direcotries, you may try 'RewriteMap' option and txt config file.

Adding this line to .htaccess:
RewriteCond %{REQUEST_FILENAME} !-d
before:
RewriteRule .* sapphire/main.php?url=%1&%{QUERY_STRING} [L]
makes SilverStripe ignore requests for existing directories.

Here is a patch for install.php that adds that line to the .htaccess file:
http://www.elijahlofgren.com/silverstripe/patches/Make-htaccess-not-process-requests-for-existing-directories-2007-06-07.patch

Hope this helps,

Elijah Lofgren