I don't see these pieces as comparing apples to apples, as I think they do different things (both well, but not the same). I have the R1; I don't have the Indie but I have other similar merino garments. The Indie is 195 g/m2 merino, meaning it is a baselayer-weight garment. The R1 is made with Polartec PowerDry, which is a lightweight gridded fleece fabric. The R1 is a much warmer garment, and suitable for colder temps than the Indie.
Personally, I'd use the Indie (or similar merino hoody, e.g. Icebreaker 200) as a hooded base layer for temps between about 40F and 15F, under a light wind shell. I would add a merino T-shirt or LS shirt underneath at the lower end of that range. Below 15, I break out the R1, with a merino t-shirt or long sleeve shirt or hoody under it as temps dictate. Getting into negative digits, I add a fleece vest over top. All this is presuming fairly strenuous activity, of course. I live in Ottawa, Canada, so your temperature comfort ranges may differ from mine depending where you are and what you are used to.
The R1 is excellent for keeping you warm and wicking moisture during strenuous activity in cold temperatures, but I've found it only so-so in the odor department. I can wear my merino clothes for weeks without odor issues, but I need to wash my R1 every few times I wear it. Fantastic garment, though.