The only problem you may have in multi-forest environments -- CDP/AIA URL reachability from each forest. The problem is greatly reduced if you do not use LDAP URLs in CDP/AIA extension for all CAs in the chain. In this case, you don't need to configure
certutil -setreg ca\DSConfigDN entry. It won't be used.
What you will need -- is a shared HTTP web server where your root CA will host its CRT/CRL files. This HTTP endpoint must be reachable from both forests.
Further, I would recommend to read my blog post on this subject which explains best practices on how to properly design CDP/AIA extensions on your CAs and avoid issues you entered in this thread: Designing CRL Distribution Points and Authority Information Access locations