The signal quality of each transponder is affected by many variables as you mention. Add to the list, adjacent satellite interference, reflector, feed, LNB and receiver characteristics.
A link budget is developed for each carrier that is based on the downlink requirements for maintaining a margin of signal strength for xx.x% reliability. This includes the amount of money the broadcaster wishes to spend, bandwidth, dish size, efficiency, prevailing weather conditions, uptime, etc.
Example: if the target downlinks have large efficient dishes/feeds and generally great weather, the link may use a higher FEC, less bandwidth and lower power to achieve acceptable up-time. Downlinks operating outside of the link budget calculations will experience lower quality levels and reduced up-time.