That's exactly right.
No software 'requires' ioncube. The coder made a judgement call to obfuscate data. Usually this is done to obscure methodology (for whatever reason). Some scripts use it to protect copywritten content, others use it to hide the fact they've ripped off other's code, and the worst hide their evilness inside the encrypted bits.
They're the ones that don't "require" ioncube, fopen, register globals, etc.
There are multiple solutions on the page you linked, which one did you attempt?
Notepad them. What's the difference between the info.php and phpinfo.php you allude to?
Perhaps PHP is being directed to an incorrect location.
I couldn't make a call on that without clearer information.
No reboot is required as DH uses the better approach. (See ioncube site re: runtime).
To which instructions regarding a reboot are you referring?
Very Carefully delete all files the installation(s) created within root and domain.com, including directories, with the command rm -rf dirname. You can ascertain the directories & files created by reading the script(s) you used. Most scripts appear to rely on an etc folder, so be sure there aren't any files in there that don't pertain to your customised PHP before removing it from root. You wouldn't want to inadvertently break something else whilst endeavouring to fix this (something I've learned the hard way - a few times lol).
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