It's no surprise to me that the higher-level items are more expensive, so could I expect to be making at least 2k crowns a run sometime soon? I am currently Knight rank.
Does the crowns-per-run ratio increase as you level up?
The tiers (1, 2, 3) increase in payout as you go deeper. Also, the second stratum of each tier pays much more than the first. In fact, the latter effect tends to be bigger than the former, so that the highest paying stratum is 6, then maybe 4, 5, 2-and-3 (close to tie?), and then 1. On the other hand, running the first stratum in a tier gets you to Basil, where you may be able to buy a rare recipe, to sell at a big profit later.
A similar phenomenon holds in missions. You can see detailed data on those payouts (not yet updated for difficulty levels, but still a good guide).
Oh wow, that's a really epic chart... how many trials did you guys do to make it and are there plans to make a better one now that elite mode is out?
Yeah, it's a lot of data. For each mission, the "N" column tells you how many data there are, roughly. (It actually tells you how many spark data there are. The number of crown data is at least this big.)
I haven't spoken with Donkeyhaute in a while, but last time he said that they were hoping to avoid collecting all-new data on all three difficulty levels. They were going to pick specific missions, to tease out the payout difference between Advanced and Normal, and between Advanced and Elite. And then just use that to extrapolate. The variation in payouts for a mission, even within the "classic" difficulty level, is so wide that there's no point in getting too precise.
Deeper/harder levels give more crowns as a general rule, yes.