Glad you have a solution.
Some notes on how things work:
The thing that everyone is dancing around, but not explicitly saying is
that characters and fonts/font effects are two separate things. Each
character is just a "plain" character. Various programs can be used to add
effects such as font, rotation, size, italic, ... These are generally
accomplished by either applying them to an entire body of text or by
embedding special formatting codes within the text itself.
These codes need to be invisible to the user, so the text file must have
some additional structure to support them. This is why they won't work in
a text editor - which assumes plain text with no additional structure.
Since there is no universal representation of fonts and font effects, each
class of programs represents them in a different way and has different
ways of setting and resetting them.
Handling this in AutoKey is most easily accomplished using scripts as has
been covered in the other posts.
However, if you really want to, you can do it in phrases as well by
including macros in your phrase for things like <ctrl>+i or even
<codexx>. For these to work, you need to specify the Paste using keyboard
option. This is fine as long as all your characters are in the EN-US
locale code page and assigned to existing keyboard keys. If not, it
becomes rather tortuous to accomplish.
Joe
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