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Admin Tools knows what the .htaccess file should look like when it's create by the .htaccess Maker feature. It compares that against what you have on disk. When it differs, it tells you that you need to create it afresh. The idea is that if we make changes in how this file is generated to improve performance or address issues you would be unaware – nobody reads the release notes.

JCH Optimize adds stuff to your .htaccess file on disk. Therefore, the on-disk state drifts from what Admin Tools knows the file should look like, causing the message to appear.

Here's the thing. What you are doing is wrong. You don't need JCH Optimize to modify your file. These rules exist in the .htaccess Maker. Moreover, the .htaccess Maker – unlike JCH Optimize – does not put a self-advertising HTTP header.

I have a security concern with JCH Optimize's self-advertising header. It not only says that you are using that software on your site, it reports the exact version. This is fingerprinting. If there's ever a security issue in that software, attackers will be able to very trivially identify not only the population of sites using that software, but also the exact sites using the vulnerable versions. To be clear, the lack of a self-advertising HTTP header / page output with the exact version number doesn't increase a site's security, but the presence of the same has a well-understood security impact.

Remember, that's that entire reason why Admin Tools lets you scrub Apache's and PHP's self-advertising (Powered-By) HTTP header with the “Remove web server and PHP version signature”. Doing that, but having some extension provide its own self-advertising header is a security concern you should be aware of.