I think you nailed it right on the head with your Universal comparison. There is something very timeless in the way a Toho film is made, in any era. Your absolutely right, too. I was watching Matango the other day and I could totally feel where you were coming from. It felt like I was watching a movie in a very comfortable surrounding. Even though the characters and actors were unfamiliar too me, and they were portraying the most horrendous people imaginable, it still felt right.
Toho movies also feel like they can all be part of the same universe. Matango can take place in the same universe as Godzilla movies and likewise with the Frankenstein films. When they added the Gargantuans to the story in GXMG it felt totally right. Like they belong in Godzilla's history.
I consider Gamera: Guardian of the Universe to be second only to Gojira as the GREATEST Kaiju film ever made. Yet, it still doesn't have that something special that makes it a Toho movie, because it just isn't, it feels different.
That is my take anyway.
Same as your really.
-Ray