I bought some 3.3 LDOs (MIC2940A), and I'm now using that to regulate the 5V rail coming out of my wall wart for my 3.3V bus, rather than using the 3V rail on my dev board. I couldn't find the part in KiCad, so I just wired up another LDO and renamed it.
I also significantly shortened the jumpers from dev board to breadboard, and I replaced all the breadboard jumpers with wires I cut myself.
Chalcogenide had some good advice that PD6 on my MCU was 5V tolerant, so I am connecting my TSOP sensor to the 5V rail now and just feeding that into PD6. I thought this might resolve the issue entirely since I thought VDD for my board would still be 3V, and therefore VIH would be 0.7*3.3 = 2.3V. When I checked my scope, my power rail was still rippling, but seemingly never below 3V. For some reason, my MCU was still detecting these ripples as edges. Unsure the reasoning behind that.
Either way, with the power of all this advice combined, I am now able to drive the motor with up to 80% duty cycle PWM without the IR receiver getting tripped. That feels like a victory in and of itself XD. I've learned a lot so far, and I've especially learned that cheap DC motors and cheap IR receivers don't play nice haha.