I haven't tested this with exact versions, so this is a bit theoretical at this point. However I'm fairly confident this could cause some hard to notice / track down issues.

Steps to reproduce:

1. Install an older release, EG 2017.2
2. Reset user config to factory defaults, to ensure that the config schema is for 2017.2
3. Open the NVDA config file, and take note of the schema version
4. Run from the launcher of a newer release EG 2017.3
5. Don't install the newer release, decide to continue using the already installed older release.
6. Check the config schema version

Expected behavior:

The config file should remain as it was in the 2017.2 install, and not be affected by running from the launcher.
This goes for voice dictionary files as well.

Actual behavior:

Its likely that the config files get upgraded to the new schema. These changes are not necessarily backwards compatible, and might result in certain settings mysteriously different after running from the launcher. One example is the braille display cursor blink rate.
Moving the voice dictionary files could result in these files not being available anymore in the older install.