Many popular apps fail to verify using bundletool 1.18.3

**Describe the bug**
If you use bundletool 1.18.3 with the following command:

```bash
bundletool check-transparency \
--mode=connected_device \
--package-name=""
```

With any of these popular apps:
- Signal: org.thoughtcrime.securesms
- WhatsApp: com.whatsapp
- Messenger: com.facebook.orca

You'll get this error:

```bash
Verification failed: APK signature invalid for base.apk
```

**Bundletool version(s) affected**
Version: 1.18.3

**Stacktrace**
None

**To Reproduce**
```bash
bundletool check-transparency \
--mode=connected_device \
--package-name=""
```

**Expected behavior**
I would expect it to verify

**Known workaround**
If you apply [this PR](https://github.com/google/bundletool/pull/368) my colleague made to update apksig, everything works.

**Environment:**
OS: Ubuntu 24.03, but I suspect this doesn't matter

**Additional context**
Add any other context about the problem here.