It's not intuitive to have to refresh an Input Step to get new files included in a wildcard union. It's different behavior from Tableau Desktop. And it's a pain to have to remember to click "Refresh" to have new files included. Many users have files that are dumped into a directory on some sort of periodic basis (hourly, daily, weekly) and expect that these become part of the source data for a flow.
The worst part of the current behavior is when it comes to automating the running of flows. I'm super excited to see options for running a flow via command line now available and am anticipating more automating/scheduling options in the future.
Unfortunately, I'm not able to take advantage of this feature in several cases because there's not an option to allow wildcard unions to automatically refresh the files that are included. Right now, it seems that running a flow via the command line interface does not refresh the files included in a wildcard union. That means it's still a manual process of opening the flow, clicking Refresh, and then running it. At the very least, there needs to be an option for the command-line execution to force the refresh of the input nodes / data sources (and corresponding options for any other scheduling capabilities that come in the future). But even better, in my opinion, the behavior should change completely to be more automatic and intuitive.
(if it feels necessary to retain the current behavior for some users who might want it - though I don't see any reason they should - then consider including a checkbox / toggle switch option in Tableau Prep if some users want to prevent the auto-refresh on loading the flow and possibly make that the default for legacy flows)