Some work-arounds:

• Use #exec cgi,
• If the params are known in advance, use something like #include virtual="script?id=$id&other=$other"
• Possible, but untested: maybe use #include virtual="script?$QUERY_STRING" to pass off the query string as parsed for the X-SSI?

The latter two assume that something like #echo var="QUERY_STRING" or #echo var="id" work in your X-SSI normally.

What I suspect Apache is doing is giving the X-SSI "subshell" (whatever) the query, so you can do simple stuff like #echo var or #if/#else/#endif, so it doesn't propagate that to the script's environment; that gives you the ability to do #include virtual="otherscript?new-param=unrelated-value (like #include virtual="sidebar?site-section=frontdoor&style=blue") which might not depend upon the $QUERY_STRING's contents