Research indicates that multiple people on this very forum run 6x9s without adapters because the adapters cause clearance issues with the trunk rods. Those people seem to like mounting the speakers from below, and that's my plan since I wish the leave the package tray unmolested. Cutting it up sounds like a bad idea that's hard to un-do so instead you might mount a piece of wood or metal plate with a cutout that matches the stock hole to the package tray from above, and add studs to that piece so the 6x9 is easy to hang from below. Then everything is removable without any real damage. It's easier to live with drilling holes to accommodate the studs than a butchered tray. An alternative is simply welding the studs directly to the package tray itself from above, and bag of button head machine screws works if they're the right material.
Cutting the rear seat back sheetmetal seems to be necessary for clearance, and that info also came from old threads. I highly suggest checking the mounting depth of the speakers you want to use and comparing that to the clearance available- some newer models use much smaller magnets. Be sure to avoid pinching or blocking the rubber surround for the speaker when you mount it or it'll negatively affect sound/ you can tear it.
Cutting the rear seat back sheetmetal seems to be necessary for clearance, and that info also came from old threads. I highly suggest checking the mounting depth of the speakers you want to use and comparing that to the clearance available- some newer models use much smaller magnets. Be sure to avoid pinching or blocking the rubber surround for the speaker when you mount it or it'll negatively affect sound/ you can tear it.