The integrated shelf probably has the better thermal path, but I don’t think it would make a significant difference in the performance of the light. I say this based on measurements that I have done which show the thermal path of a light is usually not the “bottleneck”. The limiting factors for heat management is the light’s small thermal mass and small surface area, and the integrated shelf doesn’t help with those.
Edit: the above statements do depend on the power of the emitter you put in there. What do you plan to use?
I think the practical differences are going to have to do with ease of modification and use. Having a pill makes it a bit easier to solder things on, and it allows for the possibility of having multiple pills for the light. I don’t have the integrated shelf S3, so maybe someone else can identify other pros and cons.