I'm not an instructor yet, but I can give you my point of view on doing multiple flights per day during my instrument and commercial training.

When I was a private student, my instructor never let me do more than one flight per day, and looking back that was definitely good advice for me.

Once I got into instrument rating I was at a different school that allowed us to schedule whenever and however many times a day we wanted. During instrument I doubled up flights here and there and didn't really have any problems until I got into the real meat of instrument approaches, then I felt like the second flight of the day was just too much.

When I got into commercial, I typically did two flights a day. I was doing my multi engine and single engine commercial at the same time, so I'd typically do a single engine flight and a multi flight each day to mix it up a bit. Personally, as long as I had a break in between the flights I always felt like I got 100% out of my flights, and I'm pretty sure my instructor would attest to that. Once I did 4 flights in one day, and I did 3 flights in one day a couple times, and that was more than my limit.

I really think it depends on the student, but I felt like I benefitted from doing multiple flights per day. I finished my instrument in just under 40 hours (15ish hours of sim time and the rest plane) and my multi and single commercial I got in 122 hours out of 120, partially due to the fact that my single add-one checkride kept getting delayed due to weather.