If you are going to include VFL flags then maybe you have to include WAFL and SANFL flags for Port and Freo before they entered the AFL.
Now there's a can of worms.
Let's have a good look at this.
For a start the VFL became the AFL. The AFL was not formed by an amalgamation of the WAFL, SANFL and VFL - it only came from the VFL.
Next up: West Coast, Fremantle, Port Power and Adelaide were never in any other league so they get no flags because . . . they have no flags.
The argument about VFA flags is similarly flawed. The VFA back when Geelong won a few would have barely had an organised fixture and you would need to put a cut off date well after 1877 to make this reasonable. Where do you draw the line? Too difficult. In saying this we lose 2 flags we won in the VFA after the VFL was formed.
The one that I do have trouble with is whether Fitzroy flags count for the Brisbane Lions. A lot of lists have Brisbane on 3 flags. I disagree, that was a merging of the Brisbane Bears and the Fitzroy Football Club - they get all flags from both sides before the merger, plus the post merger flags, that makes 11 from memory.
DS