Getting very high scores on the daily run depends a lot on luck and the modifiers, but these are some things that are necessary regardless of the run. 40,000 points isn't too difficult if you follow these tips, though 50k does require pretty much everything to go right for you and to have a near-perfect run.
1) Do every optional challenge on non-boss battles - There are no achievements for winning runs, so you need to go all in on score. I am pretty sure it is impossible to score 50,000 if you skip even one. Each optional challenge gives a 50% score boost and a coin/unit/artifact reward, so even if you take some pyre damage it will be a net positive.
2) Build around getting early kills on bosses - There are huge score boosts for killing the 3 main bosses before the final phase. The earlier the kill, the higher the bonus. As you are building your deck look for cards/combos that will make this possible.
3) Try to have coins left over after the Seraph battle - This is the least important factor, but you do get an additional point for each coin remaining at the end of the run. This can push you over the 30/40/50K threshold, and might even be necessary for 50k. Only spend your coins when necessary or when the purchase makes an early boss kill more likely, especially in the final area.
4) Avoid taking pyre damage whenever possible - You can't use your health as a resource like you can in other card games without taking significant score penalties, capping at a 50% reduction.
5) Try to kill minor bosses on the bottom floor - While top floor strategies tend to be a bit safer, killing minor bosses on lower floors gives a significant score bonus. (30% bottom, 20% mid, 10% top, 0% pyre). While this might not be possible sometimes with certain bosses, namely the stealth one, try to plan your kill on as low a floor as possible.