IBM System/38, evolved into AS/400 and IBM i, is one of architectures described in this book:
https://homes.cs.washington.edu/~levy/capabook/
Far as language-based security, the first mainframe for businesses used a high-level language combined with a CPU that dynamically checked the programs. Still sold by Unisys but I doubt hardware checks still exist.
http://www.smecc.org/The%20Architecture%20%20of%20the%20Burr...
The Flex Machine implemented capabilities and trusted procedures in the microcode:
https://en.wikipedia.org/wiki/Flex_machine
ASOS supported a mix of methods where each app was Ada for its safety features but a MLS kernel modeled in Gypsy separated various security levels:
https://pdfs.semanticscholar.org/42a4/e6f812538c18461277c58a...
SAFE explored tagging at CPU level which got commercialized as CoreGuard or Inherently Secure Processor:
http://www.crash-safe.org/papers.html
https://www.draper.com/explore-solutions/inherently-secure-p...
In embedded, there's Java processors that run bytecode natively with some support for separation. They blur the line between VM's and native apps:
http://ajile.com/index.php?option=com_content&view=article&i...
AS/400 though does use hardware heavily in it's isolation model, going so far as to have a custom PowerPC variant currently that adds tagged memory.
And yes I call them mainframes, because it is as I always heard people referring to them during my Summer job back in the day, so the name stuck with me even it isn't correct.
System/360 had (and used) hardware privilege levels.
Seems like few of your examples involve not using hardware for process isolation. Java: no, except a few research OSes. Flash: no.