The reason for this is that Muon Software Center hasn't added support for the commercial repositories that Ubuntu Software Center can access.
Due to the fact that these repositories don't contain things that are freely distributable to anyone they don't use the standard repository format that is supported by all package managers (including Muon.) Instead they have a separate mechanism that allows the contents to be searched before the repositories are added, with a mechanism for adding the repositories and taking payment.
Currently Muon Software Center doesn't support this new type of repository and so none of the apps available from these repositories can be accessed using it. At this time you will have to use Ubuntu Software Center to get access to them.