Your question has caused me to need to correct myself. I just took the case off and tried again. Without the case, an iPhone 12 Pro fits relatively easily against the back of the bag (or front, I imagine). Since the official Apple case is of such negligible thickness, I found this curious and tried again with the case on. Turns out that it does fit along the back edge without angling, however when one then closes and secures the flap, the top corners of the phone bulge the sides near the sangles a bit (much more so than when without the case). I did feel like I was almost scratching the inside of the bag with my (very short trimmed) nails each time I arranged my phone though which was making me nervous.
In conclusion, case or no case, the iPhone 12 Pro fits both straight against the back or at an angle. For me, keeping it at an angle makes it easier to grab without scratching the bag and also keeps the other items secured in their own little areas but I could close the bag with the lipstick included, when the phone case is removed. No matter how you put the phone, it’s still annoying to put it back and rearrange anything else inside to the correct position so I will likely continue to hand carry my phone and leave the bag space for less often used items like cards, cash, and makeup.