I followed through a selection of bugs to get here. Is there a work around for even 1 repository? I take it that I should configure Trac to default URLs without a repository name to be the repository I care about most of all.

In my opinion the repository must be added at the end of the url e.g.:

Current: [TRAC-URL]/changeset/6125e371601ae14ad41acf320b3fa7bc98ed484e
Should: [TRAC-URL]/changeset/6125e371601ae14ad41acf320b3fa7bc98ed484e/MyRepo

If I add "/MyRepo" to the url it works as it should

I agree with Roman80. Always adding the "/MyRepo" to the end of the URL would solve the issue. This would need to follow each repository that is hosted, although it could be omitted for a default repo if it exists.

Always adding the repo name /MyRepo to the end works for a changeset but doesn't work for a diff link or a source file link.

I set the trac url to http://trac/MyRepo/ and used the following mod rewrite rules so far:
RewriteRule ^/MyRepo/changeset/(\d+)(/.+)?$ /changeset/$1/MyRepo$2 [L,R]
RewriteRule ^/MyRepo/browser/(.+)$ /browser/MyRepo/$1 [L,R]
RewriteRule ^/MyRepo/$ / [L,R]