I also upload to CWOP every 5 minutes. But PWSweather only pulls MADIS data between 15 to 20 minutes delayed. Much the same thing as what happens with Windy.com where uploading directly is more current and supports more features.
One difference I've noticed is that only with direct upload can you send both solar radiation and UV index. This is because CWOP only supports solar radiation.
I haven't inspected all the possible advantages to uploading directly, but one other difference right now is that my PWSweather data goes back over a year and MADIS data on PWSweather doesn't. Could be that this is only because they only now started pulling that data in but we also don't know going forward how much MADIS history there will be.
There are probably other differences that I've missed.
Also going forward I think there will be other advantages of a direct upload vs MADIS. Look in my Trello board for hints, if any of the proposed changes are accepted. Which by the was as of today is finally open for user comments (sorry I had a user posting permissions settings problem I missed).
https://trello.com/b/bPMBQj8M/pwsweather-unofficial-feedback-tracking