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What you are trying to do won't work. The code you are trying to put at the top or the bottom of the .htaccess file is Joomla!'s core SEF section. That already exists in the .htaccess file generated by Admin Tools.

If you place your code on the bottom, it will never be used.

If you place your code on the top of the file, it overrules every protection the .htaccess Maker has to offer.

If you disable mod_rewrite then of course you will get a 500 Internal Server Error as SEF URLs require mod_rewrite for them to work.

From what I see, instead of defining the problem (symptoms) and trying to solve them, you assumed the cause and we were caught in an attempt to help you resolve the assumed cause of the issue. Most likely this will end up with two dozens posts without a result, so let's take a step back, forget everything on this thread and start by defining the problem. Then we will find out the root cause and solve it.

Let's define first what "404 redirection" in your first post means so that there is some context I can work with. Is it a third party component? If so, how it is supposed to work? For example, when someone tries to access a URL which does not exist does it try to log the 404 and redirect it to that component?

Then, let's see the symptoms of the problem. When you enable SEF URLs what happens? What did you expect and what did you get?

Then, let's try to figure out if the .htaccess is to blame or if the problem lies with the 404 redirection component. Remove the .htaccess file generated by Admin Tools, upload the stock htaccess.txt bundled with Joomla! and rename that file to .htaccess. Does the 404 redirection work now?

By providing this information we will be able to know how that redirection was supposed to work, what are the symptoms and where to look for a root cause. Then, we can proceed with triangulating the root cause and solving it :)

This is not a conflict with Admin Tools Professional, it's how Joomla! works. When you enable SEF URLs, Joomla! intercepts all URLs. If it's something non-existent to your site, it throws its own, internal 404 error message. You can either use a SEF component or one of the many 404 error customisation extensions (IIRC Yireo has a nifty one) to customise Joomla!'s 404 page.

I think that the only way to achieve something like what you want is to use a third-party SEF component (sh404SEF, AceSEF) and create an article to serve as your site's 404 page, as per the component's instructions. This is as far as you can go. As you said, when you enable SEF URLs, your server's customized error pages become irrelevant and won't work. This is due to the nature of SEF URLs. A SEF URL describes a resource which doesn't exist as a file on your site. Your server, therefore, needs to "capture" the 404 errors of the requests to these non-existent resources and forward them to Joomla!. Unfortunately, this will nullify your custom 404 handling.

IMHO, the best approach, SEO-wise, is to enable SEF URLs and don't worry about custom 404 pages too much.