Isn't this already done??
I feel like I get instructions like N400FA taxi to Runway 9R via Alpha 1, Alpha, hold short runway 36 all the time...
If you did, ATC definitely was using horrid phraseology. According to the .65, you should have been given:
"N400FA, Runway 9R, taxi via Alpha One, Alpha, hold short of runway 36".
If they didn't want to give you any hold short instructions (whether it be to hold short of another runway or a taxiway), they would have told you "N400FA, taxi to runway 9R via Alpha One, Alpha."
Now with this change, it requires ATC to issue a hold short instruction for ANY runway crossing, whether it is your assigned runway, if the runway is active, inactive, or even closed.
Huge difference, and like I said, renders FAR 91.129(i) obsolete.