I come from Microsoft sculpt where the wrist rest is built to raise your wrist higher than the finger tips (reverse tilting). If you bend your wrist down (i.e. toward the desk), then your fingers naturally curl down, whereas if you raise your wrist up (like on the MS natural), then your fingers are naturally more extended. From an ergonomics perspective, it is better to have your wrist neutral or slightly raised than to have them bent down. In that case, the top row typically requires less effort than the bottom row (particularly when reverse tilted). Now whether or not that’s more comfortable also depends on how often do you encounter bigrams like ‘dr’ – or worse, ‘cr’ – on qwerty, where you have to extend index on rows above the middle finger (these are the ‘half’ and ‘full’ scissors, respectively, in layout analyzers). The discomfort of top row index often comes from these type of scissor bigrams and is alleviated when it’s possible to also extend the middle finger slightly at the same time. Curling index finger is a move more independent of middle finger placement (but that doesn’t mean less effort/stress on the tendon, particularly for wrist up folks). In other words it’s possible for a key to be both more comfortable and incur more effort/stress at the same time.

I’m not sure, from the description of your wrist rest arrangement, if you are in the ‘wrist up’ or ‘wrist down’ camp. But certainly for wrist down folks, I can imagine the bottom row being more comfortable for the index.