It will be possible to report and dismiss updates in the newer version of Mac Informer too. We didn't scrap this feature altogether, it just didn't make the cut. It will be reinstated with one of the next minor updates. I'd guess, within a month or so.
For now, you can report those via the comments, or using the 'Report a wrong version' link on the respective app page.
As for your second question, no, unfortunately it's impossible. Maintaining two separate version histories, one for the App Store version, and another for the version distributed by the devs themselves, is hardly feasible, because in most cases the two versions are updated in parallel. When we're looking for updates, we monitor both the App Store and the official websites, and we use whichever source has the newest/highest version.
If the update is free, you should be able to install it regardless of the source; it will simply replace the version you've already got. If it's a paid app, well, I'm afraid there's not much we can do: if the reported higher version is from the App Store (and you can't install it because you bought the app from the devs themselves), it's very likely that the devs have abandoned their first-party version altogether - because it's actually more profitable for them to distribute the app themselves, without paying the 30% cut to Apple; if the reported update is from the devs' website (and you can't install it because you've got the App Store version), you will have to put up with it as an early update notification - because the update will eventually hit the App Store anyway, after it passes Apple's approval process.