Yes, that is the expectation (from the branding tools guide):
You can apply your changes to new or upgrade installations. You can also apply your customizations to an existing Pulse installation without installing or upgrading Pulse. Your changes to the Pulse user interface, message text, and online Help persist through normal client software upgrades.
Unfortunately, as you are aware, sometimes software does not behave as expected. But, the deployment you do on 5.2 is expected to persist when you upgrade to 5.3. I would recommend testing to make sure, as always, that the outcome is what you expect and contact support if undesirable behavior is observed