✅ Rule acceptance tests passed.
New Errors: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
Dropped Errors: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
New Warnings: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
Dropped Warnings: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
0 out of 1479 sources (~0 %) are corrupted.
Commit: f709461
Download the full acceptance test report here (report will disappear after 90 days).
✅ Rule acceptance tests passed.

This is the Exception that caused the problem.

SEVERE: Error resolving version infojava.lang.RuntimeException: Unable to invoke no-args constructor for class org.mobilitydata.gtfsvalidator.util.VersionResolver$VersionResponse. Registering an InstanceCreator with Gson for this type may fix this problem.
	at [email protected]/com.google.gson.internal.ConstructorConstructor$14.construct(Unknown Source)
	at [email protected]/com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(Unknown Source)
	at [email protected]/com.google.gson.Gson.fromJson(Unknown Source)
	at [email protected]/com.google.gson.Gson.fromJson(Unknown Source)
	at [email protected]/org.mobilitydata.gtfsvalidator.util.VersionResolver.resolveLatestReleaseVersion(Unknown Source)
	at [email protected]/org.mobilitydata.gtfsvalidator.util.VersionResolver.lambda$resolve$0(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.UnsupportedOperationException: Cannot allocate class org.mobilitydata.gtfsvalidator.util.VersionResolver$VersionResponse
	at [email protected]/com.google.gson.internal.UnsafeAllocator$4.newInstance(Unknown Source)
	... 10 more

I suspect it has to do with the fact that the jars have to be converted to java modules to be able to use jpackage. jpackage creates the installers.
Java modules must have a different way to manage class loaders that resulted in the Exception. This is partly speculation on my part.

Addendum:
Now that I think of it, it seems that the way it was before was wrong and I don't know how it worked.
VersionResolver had a package visibility. Then how come the class could be used in a call to a method from outside the package gson.fromJson(in, VersionResponse.class) ?

✅ Rule acceptance tests passed.
New Errors: 0 out of 1477 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
Dropped Errors: 0 out of 1477 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
New Warnings: 0 out of 1477 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
Dropped Warnings: 0 out of 1477 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
2 out of 1479 sources (~0 %) are corrupted.
Corrupted sources:
us-maryland-bwi-thurgood-marshall-airport-bwi-shuttle-gtfs-490
us-massachusetts-peter-pan-gtfs-496
Commit: 69c96b6
Download the full acceptance test report here (report will disappear after 90 days).
✅ Rule acceptance tests passed.

If this really is the fix, then I'm also not sure why it worked before. Which is to say, maybe it never did in a packaged application, as you mentioned.

✅ Rule acceptance tests passed.
New Errors: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
Dropped Errors: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
New Warnings: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
Dropped Warnings: 0 out of 1479 datasets (~0%) are invalid due to code change, which is less than the provided threshold of 1%.
0 out of 1479 sources (~0 %) are corrupted.
Commit: 0129f95
Download the full acceptance test report here (report will disappear after 90 days).
✅ Rule acceptance tests passed.