Mine were also in the trunk when I bought my car. Took my car back to the dealer after about 6 months and had them installed. I figured if I paid for them I wanted them installed. Haven’t noticed a difference while driving (I don’t track it) and have not had an issue with clearance.
Wheels are Vertini rotary forged. Does not have the nite pony package. Was all white when I got it. Painted the roof and spoiler. Added carbon fiber to the side mirrors and door handles.
I went with the EOS tow hook mount. Easy install. No problems at all.
https://eosplates.com/products/2024-up-ford-mustang-tow-hook-license-plate-mount-bracket?_pos=1&_sid=dd90d948b&_ss=r
I upgraded from a 2020 Ecoboost and have the features you mentioned (auto 10 speed trans, 401A, PP, active exhaust & magneride. Also got Recaro seats). What did it for me was how smooth the car accelerated but could be a beast when I wanted. My wife still can't get over how comfortable the ride...