The two methods of uploading definitely use different code. I believe they were even pretty much written by different sets of developers also since the vB3 team was different than the vB4 team and the Basic method is from vB3 and the Advanced method is from vB4.
As for mod_security and suhosin, they are server applications that some hosts install. So, you would need to ask your host if either is installed and if you are able to disable them yourself (usually via .htaccess).
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