Yes, the break changes don't count (wording from original AFL announcement below). So I think that makes the effective cap 102 (90 + 3x4) - which I see is the maximum for some teams that you have quoted from The Age.
"THE SUBSTITUTE will be removed and the interchange cap reduced from 120 to 90 rotations per game in 2016 under changes announced to clubs on Thursday."
"The game will return to four interchange players with clubs allowed to also make changes at quarter breaks."
Sub rule abolished, interchange cap reduced - AFL.com.au
"THE SUBSTITUTE will be removed and the interchange cap reduced from 120 to 90 rotations per game in 2016 under changes announced to clubs on Thursday."
"The game will return to four interchange players with clubs allowed to also make changes at quarter breaks."
Sub rule abolished, interchange cap reduced - AFL.com.au

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