Deciding between multiple products and variants
Really it largely comes down to data/content concerns.  E.g. using one product allows you to keep all the data that is shared by those products together, and is very DRY...and changes (be it to content, pricing, shipping etc) - only need to me made in one place, versus say 3 in your example.

But the lack of linking to variants is a definite disadvantage (one expects that will come in due course, but for now..)

If the cost of the gain (one place to edit) is too high, or there isn't much data to worry about, then by all means use 3 products and one level of variants.  It's precisely this flexibility that makes Commerce so....flexible!  (And useful :) )

There's no real right or wrong, and it would be easy to test both approaches - and even put them in front of the final editors for their view.