This is looking great.

1- I left a couple of slightly more intact ruined buildings because there are numbered labels on the main overland map pointing towards a couple of ruins in moderately better condition, but I can switch them out if you want for fully ruined buildings and rubble. I can also alter the rooftops to be 'burnt out' in places on my next step.
The original setting and map for the Lost City of Gaxmoor is right after a huge battle that destroys a lot of the city. Our time-frame for this is after some small battles but before the big one. So, I like it just the way you have it.

2- do you like the frequency and style of rubble (Kier's rocks aplenty)
Perfect

3- I placed a bit of defined road, but it can be altered to be in less good condition or completely removed. My plan if you liked this underlying texture was to have some parts of it clearly washed out by the dusty land texture, something I can't do until my next step which requires texture commitment.
That sounds good.

4- do you like the pyramid? As far as I can tell the blue and white stripes were intended to be horizontal so that's what I did but it's easy to change to vertical, change the color, etc.
I like the color of the pyramid just the way it is.

5- as the GM, would you prefer to be able to remove the pyramid (which would be delivered as a transparent png) and expose the layout as part of the same map, or have the pyramid interior layout separate / its own map?
From a playability point of view on Roll20, I think it will work best to have the interior as part of the full map and then have the roof as a removable png object.

6- do you want a baked in grid or will you have the grid added in your VTT?
Personally, I prefer maps without grids. I think the maps look better without them and I don't use them in the game either. For most people who use grids in their VTTs it is better to have no grid on the map and let the VTT add the grid.

The interior layout is looking good, and I like the floor texture you are using. One of the reasons I picked this map to have you make it is that even after reading the text a couple times I couldn't visualize the layout. I figured fresh eyes would get a better perspective.

The author of this mini-adventure, Jeff Talanian, is a friend of mine who will be at the con I will be running this game for. He is also the creator of the Astonishing Swordsmen & Sorcerers of Hyperborea game system and co-authored Castle Zagyg with Gary Gygax. ( so, no pressure! )