PCBgogo

So, I recently had a small-ish batch of boards (100) + stencil made up and they didn't come back quite as expected. I've never used this manufacturer before (although they're one of the popular Chinese web based PCB services), and not sure if I should contact them about it, or if they just decided to do some magic to make my life easier w/o telling me. I double checked my gerbers via an online gerber viewer (just in case my CAD package was being odd), and they appear normal. Thought someone might be able to tell me what's going on here. (Pics attached)
First, the boards came with solder mask only over the copper traces, none on the FR4. Pads are all correct. I don't think it should seriously effect anything (and I actually kinda like the aesthetic), but just curious what might have happened / why. Wondering if this is purely because I selected yellow for the mask (and FR4 is yellowish). Just concerned the FR4 might burn / brown a bit.
Second, most - but not all - of the stencil pads came with small indents on the inner sides of the parts. Admittedly, this is the first metal stencil that I've ever had fabbed for my personal use, but I've never seen this before. Is there a name for these? I can only figure that it is a "feature" that the manufacturer went ahead and added in to help parts reflow better? Not sure why all the pads aren't like this then though... maybe an odd size?

Thanks!