Hi grantxx,
I think clear poly goes well on natural mahogany, and timbermate natural as a grain filler would work well to help level the surface. I'm not sure if I would use Natural or a slightly red fill (like Mahogany or Hardwood) - it may not matter. I used Tru-oil on a mahogany neck and it came out very vice.

You could add a small test amount of poly (or try a stain) to the bottom of the pickup route to get an idea of the colour before committing to the whole body. Even adding a small amount of water to a section of the body will allow you to see the natural colour of the wood when clear coated.

As for the binding:
if using clear coats only, then coat over the binding as well (no need to clean it off later!),
if staining, mask the binding before the staining to try to reduce the amount of stain getting onto the binding (on my SSCM-1 I added 2/3 tru-oil coats to the binding only before adding the stain - not sure if it helped or not! ). Even with masking some stain will still probably bleed onto the binding. Scraping stain off the binding is not a lot of fun in my opinion.

I'm not sure if the binding needs protecting before sanding - I didn't! Take care near the binding though.

For sanding:
Before adding the timbermate I would sand the body to 180 g, then
If only using clear poly I would sand the timbermated body with 240 g or higher before adding the clear coats.
If staining I would sand the timbermated body with 180 g to ensure the stain is taken up more evenly.

Hopefully others will add to this.