Two mini boys here. I've mostly already forgotten our puppy potty particulars, but we were on three meals daily thru six months then transitioned to two meals a day.
DH and I are on somewhat offset schedules so when they went out was not as big an issue since one of us was almost always awake.
Figuring out when to feed them was a bit more complicated. I'd get up around 9am with them, pop outside for P&P, then back in for brekkie. Neo ate readily, Remo was a challenge. Back to condo's for a bit more sleep then lunch was about 1pm, after I actually started my day. Dinner was around 7p. Last out was 2am-3am before condo time, complete with treats/small snack per our vet, so they weren't trying to sleep on an empty stomach. I don't remember ever having to take them out after condo time til Remo would start peeping (not a typo lol) in his condo around 9am.
Fast forward from six months to not so long past that, as they were physically maturing and routines were stabilized.
We still get up about 9a for the 1st P&P then come back in and sleep some more. Well, I do. They hang out with DH downstairs but still mostly napping. I get up later, fix their brekkie about noon, they go out for 2nd P&P again just before or just after. We try to walk every day and their 3rd and usually last Poop for the day comes around 3pm, during or after the walk. If we don't make the walk, the last Poop can be anytime up til condo time, which is now usually about midnite.
How they come up with three poops a day given only two meals now is a bit of a mystery but it's pretty predictable so long as we're on our regular schedule. We're fortunate to be in a house with a backyard so they're actually in and out a lot most days, monitored or accompanied and depending on weather. Still their poop times are very predictable.
Regular mealtimes will make for regular poop times. Eventually with physical maturity and regular mealtimes you'll get predictability. So, if he's now running 10+ hours from last feeding to 4am poop, push the last feeding later by 2 or so hours. And to shoot for no poop soon after bedtime, mid day meal to be 10+ hours earlier than bedtime.
Which is pretty much the times for the 3 meal schedule you mentioned trying

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Very generally:
"What is the dog digestion time?
The
dog digestion time varies, depending on factors like the dog's breed, body weight, size, health status, how much water he consumes, the type of food he's eating, and any existing conditions or illnesses he may have, according to My Pet Needs That.
Usually, your dog will digest dry dog food within eight to 10 hours of eating it, and wet dog food within four to six hours of eating it.
According to Pet Health Network, if your dog has
ingested something he perhaps should not have had, it can take 10 to 24 hours for him to excrete it. Some objects can even take months to go through the digestive process."