Add: precondition checks to functions that work with both valid company and deity

These are functions that either use ScriptObject::Command or ScriptObject::GetCompany.
This is a bit over-protective, but having the check everywhere makes it easier to
validate that no check is missing automatically instead of by review.

At this moment these checks will not do anything useful, as either IsValid or
IsDeity from ScriptCompanyMode returns true, but that will change later.

Codechange: add non-nullptr asserts in cases where it should never be nullptr

Though where similar calls are checked for nullptr as in those instances of
the use of that function it can actually return nullptr. In other words, write
down the assumption that the function never returns nullptr in an assert.

Codechange: merge guiflags and flags in settings .ini files

It was rather confusing which one was for what, especially as some
SaveLoad flags were settings-only. Clean up this mess a bit by
having only Setting flags.

Codechange: use setting name instead of index for CmdChange(Company)Setting (#9306)

This is mostly done as there are now constraints on settings.ini you might not
expected. For example, conditional settings always have to come last, as otherwise
they would influence the index.