For me, R1 is a cross-over base layer and mid layer. Patagonia certainly markets it that way with snug-fit pull-overs as base layer and looser cut full-zip cardigan-like jackets for mid layers.
I have an R1 vest that is great for just a little more warmth while walking on level or downhill sections. I often carry it as a spare layer for summer day hiking. It is killer under a wind or rain shell and much like the traditional British sweater vest.
Agreed, that it would have to be very cold to see me hiking uphill with a load and wearing the R1 as base layer. But it is perfect to layer under a shell for rest stops and camp in cool wet weather, just as I might use a sweater or sweatshirt. I have R1 tops and bottoms that make perfect cold weather pajamas, but I wouldn't normally carry them as sleep wear only and would included them as part of my layering scheme.
The benefits of fleece are breathability and the wicking, hydrophobic nature of the fabric. It is perfect for cool, wet, humid environments. It will keep a warm layer of air near the skin while moving moisture out and away.
While water may bead up on the surface for a short time in light sprinkles, fleece should never be considered as rain gear of any kind.