You've already spotted where is the indentation and the protrusion. I have plenty confidence a car interior guy familiar with soft tops will be able to make sense out of this info and tell you where it is, or not, pulling right.
Hope you are not confirming that the design of the 986 roof is different by the years. That'd be a sad news. Many guys have changed their top and surely skipped this detail (I never heard or read myself).
Regluing the roof is no use but I could be completely wrong. Like you said, with proper paddings and materials this could be accomplished but can't be a permanent fix.
Job for the "pro roof guy" I'm seeing it coming for you :/
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'97 Boxster base model 2.5L, Guards Red/Tan leather, with a new but old Alpine am/fm radio.
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