The lowest hole, Hole 6, is the most out-of-place from its acoustically correct position.
Placing a hole higher on the tube makes the note sharper, meaning to compensate you have to make the hole smaller.
That’s why Hole 6 is the smallest hole.
Makers are caught in the middle between acoustics and the size of human hands, so they compromise.
Here are some Low Ds from several makers showing that they have all arrived at more or less the same compromise position for Hole 6.
Top to bottom:
Susato
Dixon conical bore
Reyburn maple head
Reyburn Delrin head
Burke Pro Viper
Kerry Optima
MK

Acoustically ideal would be for Hole 6 to be the same size as Hole 5, placed halfway between Hole 5 and the bottom of the tube.
There you would get a powerful Low E note.
But few could reach it!
Coming from the human anatomy side, ideal ergonomically would be for Hole 6 to be as close to Hole 5 as the other fingerholes are to each other.
To be in tune Hole 6 would have to be tiny, and the Low E note would be feeble and want to jump the octave.
So we’re stuck with the compromise that all makers have arrived at.
BTW on Burke Low Ds that Low E note is noticeably weaker than its neighbours, and that’s the Pro Viper! Burke makes an EZ reach Low D with an even weaker Low E note.
My Goldie Low D has a strong Low E, and has the lower three fingerholes a bit closer-spaced than many Low Ds. MK Low Ds have exceptionally strong Low E notes, just as strong as the other notes. I have no idea how they accomplish that.
As Sedi says, using a bore that narrows towards the end, like Recorders and Baroque flutes, allows the lower-hand holes to be closer together. I think the Tony Dixon plastic conical-bore Low D is the most comfortable Low D I’ve played.
Other than that, the solution is to have a key for that Low E note. Susato makes/made Low Ds like that, they are obviously super easy to finger.
https://www.youtube.com/watch?v=JESWb8Xnmoc&t=95s
This video is very nice, he demonstrates the drawbacks to the keys, making “pats” more difficult, and eliminating the nice gliss you can do with an open hole. His Susato Low D has keys for both ring fingers, to me the upper key isn’t necessary, and a key for Low E being the only useful one.