Good Question... I had the same one for my '20 490. Here's what I found and what I did...
The early blocks and heads did not have the coolant jacket holes in either the block or the head behind #4 cylinder. As you noted, that area is prone to higher heat.
In my case, my '20 block did not have those 2 holes either. But the head had been replaced at some point in the past with a slightly newer head, 'ie. '25-'26 which did have the coolant ports. And of course, the gasket had the ports. I had pulled my head because it had a stuck valve at the time. The car had been in storage for ~40 years before I got it. So, my dilemma was the same as yours, do I drill out those ports in the block. After some consultation with others, I ended up drilling out the ports in the block.
Be sure to have a small magnet available afterward to fit through the holes and 'vacuum' up the filings from inside the water jacket. I also had a small endoscope camera to look inside closer for the filings and corrosion buildup. Not necessary, but certainly helpful in this case. I had the water pump off mine at the time too. Your '16 would not have the water pump. I then used compressed air and coat hangers to loosen up as much of the internal corrosion as I could in both the block and head.
After all that, and getting it all back together, I got it running after its long slumber, only to find out the head was cracked in the #2 exhaust chamber. Off it came again.
I had a '28 head already done and ready to go on, so that's what I did. Got it running and took it on the 4-cylinder tour a couple months later. No heating issues whatsoever.
As you're preparing to drill, be sure to mark the locations very well. I don't recall what size drill bit I used but it was the same size hole that was in the '25-'26 head. I can go measure that in the garage and post again.
Anyway, that's my experience with this same dilemma.
