Hmmm, good question!

If you print an SSI instruction directly from the CGI script, does that get converted as expected? E.g. does

print '<!--#echo var="DATE_LOCAL" -->';
output a date, or '<!--#echo…'?

I haven't used SSIs alongside EPrints, but if the above doesn't interpret the SSI instruction my guess would be the PerlResponseHandler used for CGI scripts within EPrints::Apache::Rewrite module.

I find the diagram here: https://perl.apache.org/docs/2.0/user/handlers/http.html#HTTP_Request_Cycle_Phases useful to try and work out what the difference might be between e.g. a static page+template being served compared to a cgi script.

The request for a CGI script might not trigger the SSI handler - but you may be able to add it to the stack, or a different phase (or even the output handlers).

The start of this page: https://wiki.eprints.org/w/How_to_enable_server_side_includes indicates that someone has been down this path before:
"If you want to add dynamic content to the template you should do this via a template part in cfg.d/dynamic_template.pl"

They possibly included a maintenance.ssi file using perl-based methods rather than SSI methods?

Cheers,

John