All code snippets I "winged" cmake is a little picky sometimes it wants ${var} other times var on its own is enough, you may have to play with it a little.

This doesn't scale well. A new dependency like OpenVDB/NanoVDB for volume would need an exception and its own list of tests & variables.
Instead of globbing all files under a folder, suggest doing how its done in source code. Say WITH_USD controls if usd code files are built or not.
Same for testing, tests that need GMP could be in a separate folder, with its CMakeLists.txt globbing the blend files there. Or listing manually if finer control is needed, like having another dependency alongside GMP.

I like @Ankit Meel (ankitm) 's idea

A more elegant change by sticking the two problematic files into tests\modeling\geometry_nodes\mesh\boolean\ rather than tests\modeling\geometry_nodes\mesh and having something like

diff --git a/tests/python/CMakeLists.txt b/tests/python/CMakeLists.txt
index a1b94abc317..fa7c343a053 100644
--- a/tests/python/CMakeLists.txt
+++ b/tests/python/CMakeLists.txt
@@ -751,9 +751,12 @@ set(geo_node_tests
   utilities
   vector
   volume
-
 )

+if(WITH_GMP)
+  list(APPEND geo_node_tests mesh/boolean)
+endif()
+
 foreach(geo_node_test ${geo_node_tests})
   if(EXISTS "${TEST_SRC_DIR}/modeling/geometry_nodes/${geo_node_test}/")
     file(GLOB files "${TEST_SRC_DIR}/modeling/geometry_nodes/${geo_node_test}/*.blend")

would probably do the trick nicely

Had a chat with Ray and agreed upon not putting CMake files in SVN as my last comment hinted. People don't have the SVN folder open in their editor in case something in git changes.