Flatpaks will always be a little slower, notably if you are on slow storage media.
Yes this is all native messaging I suppose. Flatpak apps can query an app list, just look at flatseal. So I think querying the installed flatpaks and handing it over to the system portal where you then choose the desired app is the modern workflow for this.
You might want to request that Digikam etc. implement portals for this file opening. Firefox can do for example but of course these are limited as long as apps dont modernize their workflow