The 5x7” driver side 1/4-3/8” drop down stamped into the package tray will indeed physically interfere with most aftermarket quality 6x9” surround and woofer cones without the use of a spacer of some kind. Again most high end 6x9”s will come with a spacer thick enough for a flush mount but are not tall enough to provide clearance for a drop down stamping that would fit inside the circumference of the speaker frame. Clearly the OP is no longer referring to “regular” aftermarket single cone speakers that may or may not clear the drop down. Frankly, the correct approach, from a pure performance standpoint, would be to cut out the drop down and the smaller restrictive 5x7” opening anyway if installing a 6x9”. The area of the opening shouldn’t be less than the area of the woofer cone.
Still need a spacer? Stop by your local car stereo installation shop, they will likely have leftovers from previous installations in varying heights.