Well , i'll get into this as well and from my disccusion with Nicolas from Akeeba:
Ever since Joomla! 1.5 –released 18 (eighteen) years ago in 2007– the recommendation has been that extensions should place their static media files in a subdirectory of the media folder named after the extension. This has always been a security-focused recommendation. Do note that Joomla! 1.5 did not enforce the naming of the media subdirectory. Joomla 1.6/1.7/2.5 did enforce the naming of the media subdirectory and defaulted to it.
Ever since Joomla! 3.0 –released 13 (thirteen) years ago in 2012– the recommendation was upgraded to a reasonable expectation. In other words, it was reasonably expected and assumed that all extensions which are fully compatible with Joomla 3.x will follow this scheme for placing their media files in a correctly named media subdirectory. While one could work around that, it was strongly discouraged. The old methods for circumventing the use of a media subdirectory were marked as deprecated about ~8 years ago.
As of Joomla! 4.0 –released four and a half years ago in 2021– using a subdirectory of the media folder named after the extension is mandatory for all extensions as a very much intended consequence of introducing the WebAssetManager.
Since Joomla 4.2 –released in 2022– it is also mandatory for templates to place their static media files in a subdirectory of media/templates. This is an intended consequence of child templates.
Since Joomla 5.0 –released in 2023– deviation of these mandatory requirements is considered a show stopper bug of the extension. This is an intended consequence of the public folder feature being introduced. The code to work around the media subdirectory requirement was removed from Joomla.
Helix developers should have known that:
for the past 18 years (predating their template's existence) their system template should be putting its media files under media/plg_system_helixultimate.
for the past three years their template should be putting its static media files under media/templates/site/TEMPLATE_NAME where TEMPLATE_NAME is the name of the template (without the tpl_ prefix).
Their template is not following Joomla's standards. It violates the static media files placement requirement which is in place for very good security reasons.
The .htaccess Maker will only include default settings which allow extensions following Joomla's very reasonable security standards to function properly, without having to do any configuration changes. Extensions like Helix Ultimate which DO NOT follow Joomla's security standards will always require additional configuration.
Alternatively, JoomShaper should shape up (pun intended) their code so that it follows a Joomla standard that's been around longer than their company or, indeed, Admin Tools itself. If they do that then their template will work without any configuration change whatsoever to the out-of-the-box settings of the .htaccess Maker. It will also allow their users to create child templates, and it would allow them developers to deliver versions of their template compatible with newer Joomla releases faster as there would be one less security control in Joomla they have to figure out how to circumvent every single time there's a new Joomla version. In short, it's absolutely bonkers that for well over a decade they flat out refuse to fix their code to follow Joomla's standards.