I’ll respond to all three questions in one,
- We use masks whenever theres the slight possibility that I will need the rest of the layer later on, or I will need to give it a feathering that I can adjust to fit my needs.
When using the replace color tool it would not be necessary to use a mask as you are not cutting a layer, you can duplicate the layer below if you want to have a “back up” of the file. But a mask would not be necessary.
Working with a clipping path vs a mask layer will visually give you the same result the only difference is how easily you can adjust. As a clipping mask you can move one layer (the content) layer without moving the logo layer (the container)
Yes the fill goes above the container inside of photoshop where in illustrator it goes below- the result is the same though, content is always put into a container