I initially reported this as a bug on the support forums but after reading the announcement post, I see this is expected behaviour.

Actually that is a bug, and we're looking into it, thanks for the report.

PNG icons will stand out in the otherwise color-unified MP6 look, especially when you pick a color scheme other than the default. But we did not intend to block anyone from using PNG icons, they should still work as the usual. MP6 is still in beta, this one slipped through the cracks.

To take advantage of the SVG painter that'll paint icons to match the users color scheme, we do strongly encourage plugin developers to update their icons. Here are three methods of providing such an icon: https://github.com/tillkruess/MP6-Icon-Examples