Also it may worth implementing some sort of exceptions... to ignore properties like Enabled or Active which are often used in this kind of assignments. What do you think about it?

You can use _FIXINSIGHT_ compiler directive. It works just like a real compiler conditional. For instance,

{$IFNDEF _FIXINSIGHT_}
procedure RestartTimer;
begin // this code will be ignored
  FTimer.Enabled := False;
  FTimer.Enabled := True;
end;
{$ENDIF}

This functionality is rather primitive though. It allows you to turn off any analysis, not only a single warning. A more comprehensive approach is still in the development. It will be available in future releases.

I will fix this in the next release.

Oops, typo! Fixed.

Analyzing new apps (just created) is an another issue
http://fixinsight.userecho.com/topic/632361-new-units-are-not-taken-into-account/
:)

That should not depend on Delphi version. But this is a good point. I'll check it with XE5.

Hm. Interesting. For me it doesn't produce a warning for this code.
OK, I will spend more time debugging this rule.