@Switch Blayde
For example, if I'm working on a novel I use Word's italics. If I'm working on a story for SOL I put the < i > before and after the italicized word(s).
This is why I separate my layout from my markup, if I can use those terms. I write in a text editor (BBEdit) which is extremely lightweight and doesn't care if I have my entire series open at once. It supports folders and hierarchies, making organization easy. I use only a few of the basic SOL markup indicators (_, *, {tt}). This allows me to do literally anything with it.
When I need to create an eBook, I run a bash/zsh script to turn those markups into markdown, then import into Scrivener which has all the layout and formatting tools, and I've created a custom set for my novels. The process of going from the lightweight text editor to the ePub is literally less than two minutes, plus the time to generate the ePub.
BBEdit is free (if you don't need the advanced features) and has fantastic search and replace features, including 'grep' style search and regular expressions. If you're a coder, it has an amazing set of coder support (folding, color-coding, git, etc).
Of course, I'm on a Mac, so YMMV.