There is a difference between the "boot" and "well liner". You might be using "boot" to mean "well liner"?
To me, the well liner will always stay in place and separate the top from what's in the luggage compartment, including being a water shield of sorts.
What I'd term "boot" would be the cover that snaps over the lowered top assy for looks and suich.
Be sure to locate any body water drains in the c-pillar area and make sure they are open. With the top fully raised, the c-pillar fabric should "seal" against the outer edges of the surround moldings and trim, typically, but those drains are necessary should any moisture get past the fabric. Not unlike factory sunroofs having drains at each of their corners, too.
Everything looks good, so far.
CBODY67