Yes it will affect the output levels. The IR sensor output is referenced to 5V but the ADC on the Duet is referenced to 3.3V. the 1.04 Duet is OK with up to 5V going into the Zprobe input, but you will have to see what the actual Z probew readings are. Instead if being about 465 and 535 (allowing you to use 500 as the threshold), they will be about 51.5% higher. You will need to adjust the threshold accordingly.
Alternatively, use a 3.3v regulator on the print carriage, for example one of these if you want something easy to solder https://www.mouser.co.uk/Semiconductors/Power-Management-ICs/_/N-wnwh?P=1z0wa2eZ1z0z60lZ1z0y3js.
