Tesla wants their Signature cars to look and perform as the top of their range. If you want a different spec then just order what you want. IMO (no offence intended!) it sounds like you want the Sig badges but with your own spec and at a lower price. I respect that but from a marketing standpoint it doesn't make sense for Tesla to encourage that.
Actually, I'm largely trying to understand (and/or critique) the rationale behind their choices. I think such things should have a clear vision, a reflection of the company's values or goals.
Tesla's Sig pricing, as it stands, is full of contradictions. The pano roof is an option, leather/charger/etc isn't. Some things are options that you don't start with, but cost to get. Other options you start with, but don't get credit when removed.
The pano roof and paint is a great example of the inconsistentcy. Both are $1500, yet they're treated differently. Why wouldn't the pano-roof be standard and the black/solid roof a "no cost" option? That'd be consistent with how the paint option is handled.
I'd actually be fine if Tesla had said "every option, full price, no credit for downgrades, no exception" as that's a clear vision about their intent for the Sig. I wouldn't be interested and I'd disagree on the ethics of "no credit for downgrades", but I could respect the vision behind it.
We can certainly say "it is what it is", but right now the vision is muddy. Are they focused on the customer? On the initial assembly variations? On the bottom line? On the word of mouth impressions inherent in the Sigs? Given the options/pricing as it stands, I could argue for or against all of those. There's undoubtedly some balance, but whatever balance considerations drove the current choices is opaque at best.
Edit: Cobos mostly beat me to it and hit the nail on the head.