Thank you, for an awesome app on macOS as well as on iOS and thoughtful support. :-)
I totally get where you're coming from. From your description, the decision made perfect sense at the time.
I think the key to this is that Emmet, as I've understood it, is a non-default plugin in those other text editors you mentioned. In those editors, the user explicitly elected to use Emmet, along with its shortcuts. As someone who has never used Emmet, I've never had any issues using Emacs style Ctrl+A and Ctrl+E in neither Atom nor Sublime Text (in their default configurations).
Since you've had the Emmet shortcuts enabled in Textastic for some time, you risk confusion existing users of Emmet in Textastic if you disable them by default (while keeping Emmet enabled). At the same time, you risk alienating new users of Textastic having the Emmet shortcuts enabled by default.
Therefore, I still think that adding an option to disabled Emmet completly makes most sense. That way the user can choose to use Emmet, along with its shortcuts, or not. By disabling Emmet by default, and having an option in Preferences to enable it, you don't risk confusing neither Emmet nor Emacs shortcut users. Since Emmet is a plugin in other well known editors, enabling/disabling Emmet as a plugin in Textastic is intuitive. Users experienced enough to use the Emmet plugin, will know to look in the preferences to enable it.
This decades old Emacs/macOS/Unix Ctrl+A and Ctrl+E convention is used pretty much everywhere for text editing in macOS. Changing the default text editing behavior for Ctrl+A and Ctrl+E is not at all intuitive for text editor users on macOS, and I would thus argue that this is a UX bug.
This bug really tripped me up. I couldn't use Textastic productively on macOS, until I found this thread and its workaround. I'm probably not alone. It's a shame on an otherwise terrific text editor. Most ironic and confusing of all, you can by default use Emacs Ctrl+A and Ctrl+E when editing text in the Textastic preferences, but not when editing text in the actual text editor.
An option to completely disable Emmet in Textastic, and thus get standard Emacs/macOS/Unix Ctrl+A and Ctrl+E behavior without any workarounds would be greatly appreciated. It's annoying and error prone having to deploy workarounds, to get standard macOS text editing behavior in a text editor, on every macOS system where you wish to use Textastic.
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