Training wheels:
They're good questions. Google "CASA part 61" revealed a number of results, including FAQs, a sample license, a Part 61 summary booklet and of course the text of the rule itself.
Here's what I learned.
There are no sticky labels. It all goes in your license (ratings & endorsements and proficiency checks.)
It appears that approvals for VOR, NDB etc cease to exist except for pIR holders. The full IR just has 2D & 3D approaches. So, I suppose that an NDB approach covers you for a VOR approach as well, at least for 90 day currency. (I certainly hope so. Reduced regulatory burden.)
How does one get trained & tested for all the different types of navaid? Presumably the traditional way, but I haven't checked. The MOS was in the list of Google results though...