NOBODY will ever be happy to play in an 'alternate' strip - it's an alternate!!! - what you use when you can't use the one you want.
But, it has to happen. You're right about the main problem - the AFL rules are pathetic about it. Make the rules - unambiguous - list all the clashes, and what team has precedence (home team, highest team, whatever), and how the clashes are to be solved (alternate strip, white shorts, whatever). Before the start of 2018, thanks.
Anyone remember the famous Port v Richmond EF of 2014, where the AFL pulled a ruling out of their a*se in the week of the game, that eventually wound up with the away team wearing their home strip, and Port wearing a strip they weren't technically approved to wear in the AFL (not that anyone really minded that, but......).