Repro:

• download the server jar from here https://piston-data.mojang.com/v1/objects/e003d151668a0eff64c1191972707655e341f8f5/server.jar
• create a datapack (or download my example) and place it in a testpacks folder next to the jar.
• run "java -DbundlerMainClass="net.minecraft.gametest.Main" -jar server.jar --packs testpacks --report=test.xml"
• observe that the output doesn't mention your datapack

this is what I see

[20:03:19] [main/INFO]: Running GameTestMain with cwd 'F:\Projects\PaperTooling\mache\versions\25w03a\test', universe path 'gametestserver'
[20:03:24] [main/INFO]: Loaded 1372 recipes

this is what I want to see

[20:03:19] [main/INFO]: Running GameTestMain with cwd 'F:\Projects\PaperTooling\mache\versions\25w03a\test', universe path 'gametestserver'
[20:03:23] [main/INFO]: Included zip pack  mini.zip
[20:03:24] [main/INFO]: Loaded 1372 recipes

code analysis: 

GameTestMainUtil#copyPacks has the bug, this is wrong:

} else if (path2.endsWith(".zip")) {

this is the fix:

} else if (path2.toString().endsWith(".zip")) {

additionally, in the log about the zip pack an extra space sneaked in