It's impossible to give any universally applicable rules in this matter, but a couple of observations are borne out pretty consistently by the market:
1. Scott stamp valuations for "on cover" stamps are generally too high (even by 100% or more) for average usages, and they can be much too low for the exceptional usages.
2. While it is true that postal-historical characteristics loom larger than stamp characteristics in assessing cover values, don't forget that stamps well placed on cover have been less subject to perf abuse and creasing, as well as reperforation; they won't have hinging thins, and will more readily display anomalies such as cancel bleaching. So a very average cover may carry a comparatively desirable stamp.
3. There is no substitute for thorough acquaintance with the market -- that's
ebay for low-end material, and auction houses for middle and high-end material. By the time you have viewed 200 lots in 20 different nationwide auctions you will have a good sense of what prices are being paid for any given stamp on cover -- and the pre-auction estimates provided by the auction firms will be seen to have been similarly informed (notwithstanding occasional big surprises).