Run delay only applies to running the flow via the debugger (from within the flow designer). If you run your flow from the console (which is the way it is supposed to be run), Run delay does not apply at all.
Server throttles is not something you can control. The only way to avoid it, I guess, is adding some Wait actions in your flow to make it run slower.
If it's a web page, you might also be able to do it by using some Proxy IP addresses, so that the server does not realize you're accessing it from the same IP address frequently.
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