There is no difference in developing reports between the two different methods of accessing Power BI Desktop as long as they are both up-to-date. The Microsoft Store version of Power BI Desktop gives you a hassle-free auto-update, versus the download link, gives you the flexibility to install it everywhere you want.
Also, Microsoft releases additional versions throughout the month for bug fixes, so installing PowerBI Desktop via the Windows 10 Store ensures your on the latest released version automatically.
There is one important difference to be aware of - if you might have a need to roll back to a previous version of Power BI, that is easy to do with the direct download, but not with the app.
@BrianJ this is very true - but the good news is that you can have both the Windows Store version and the version that requires manual updates installed at the same time.
You just have to keep in mind which version you have open to prevent any potential problems with measure or feature availability
That is something I have not tested @BrianJ, my normal practice is to open the application, and then open the file from that.
And, I do not currently have a previous version of the program installed to test with. But this is something I found about a year ago when an update broke my Model view (it was completely blank). So I installed the previous version and then discovered that I had both the Windows Store version and the previous manual update version on my computer.
Both were usable, and the Windows Store version actually did continue to get the regular updates.