You can check the frame size of the photo in Photoshop: Image --> Image Size --> Document Size (which is different from pixel dimensions). Also note that the 35 mm X 45 mm requirement was prefaced by 'at least'. So, this does not contradict the 50 mm X 70 mm requirement set out in 5445eb.pdf document.
But, I myself have a related question regarding this. I already submitted my e-APR, with a digital photo that conforms to all the requirements set out in the e-APR uploading section (the blue dot with an exclamation mark in it).
However, the digital photo does not conform to all the requirements in the requirements set out in the 5445eb.pdf file. Specifically, in my digital photo, my mouth was slightly open, whereas in the 5445eb.pdf, it explicitly states that the mouth must be closed.
On the other hand, the e-APR instructions do not say anything about what facial expressions must be like.
I am guessing this digital photo is not that important considering that at the final stage (if one gets to that), the applicant will be asked for physical photos in the step called Passport Request.
Does anyone know whether they actually reject applications because of problems with the digital photo submitted in e-APR?