What other sites are you downloading from? They may not be able to handle as much traffic as the two stores in question.
Plus those other sites may also be trying to or actually serving up more ads, content, etc. during the download process....
Or be poorly designed and not able to "keep up" in any manner.
Are you using, for example, Windows 10 or some third party app to do the downloads?
For the most part, I would expect that Microsoft/Windows is probably designed to favor their own downloads - doing so would be in their own best interests.
Overall, there are multiple variables involved and it would take some time to truly investigate and quantify an exact reason for the lower speeds.