Is the F.Cu upper layer really on top or just the 'upper layer' but protected?
Even if you put a bit too much solder on the pad, or spill it, it won't matter. This is because of the solder mask, which is the (typically) green stuff you see on PCBs, although it can differ in colour. 

On the pads of your components, you will notice a thin purple border, which indicates the solder mask is not to go there, leaving those copper pads exposed. You seem to have a few layers with similar colours, and I don't use KiCad, but on my package it is just called the solder resist layer. 

So yes, the copper layer is just under the surface, as when it is manufactured, there will be a solder mask layer put on top, as well as any silk screen you have on there too.

There is nothing stopping you from putting a blob of solder between the resistor and the SOT23-5 pin, but I would place it close to the pad, and have a short trace connecting them.