Ηι.
but I sort of figured that somehow all great pixel art was put in mostly by hand (which always amazed me)
Don't feel bad. That's how most outside people thought about demoscene-era pixel art (which is what the indy background tutorial is attempting to look like, even if it doesn't know it). This more loose sort of 'index painting' (as in, painting with an indexed palette) is quite popular and it's very easy for the trained eye to spot where handpixelling ends and where an automatic tool is introduced.
There are advantages to index painting:
1. Faster to get somewhere where it looks like a thing
2. Easier to do some effects like smooth gradients, opacity, blur, softness, so on.
3. Looks less sharp than pixel art (some people like this) on the whole.
There are disadvantages to index painting:
1. Less control over overall palette
2. Less control over pixel placement, cluster-theory becomes more or less meaningless
3. End result occupies a somewhat uneasy aesthetic space between tight and sharp pixel art and photoshop-tooled CG (though some people, again, like this).
There are also advantages to pixelling mostly by hand:
1. More control, tighter, sharper result.
2. Superb palette control.
3. Good clusters and no banding (if you know your technique)
4. End result looks sharp and precise, i.e. "like pixel art". Not just to outsiders but insiders too.
There are disadvantages, also:
1. It takes a long time
2. It's difficult to work from general to specific like a proper painter would/should
3. The end result is usually very sharp
4. You can see where one color ends and another begins (or alternatively, you can see dithering). Some people like that, some others do not.
In the end it's not about which process (or mixture of processes) you go with, but it is about conveying to us here in Pixelation what you did and how so we can help you by having the proper information. Index painting has a bad reputation around some new-school places for one reason foremost: index painters claiming to have pixelled everything by hand. And index painters straight-up copying photos or artwork by Boris Vallejo and never mentioning it, leaving their audience to think that they came up with that stuff on their own. This artificially inflated sense of capability reeks of dishonesty. And whereas in the real art world it is very scarcely that anyone will come up to you and ask you if you've copied something, in places where learning is the goal (as pixelation), process is as important as the end result. We're not selling tickets here, we're helping each other learn. There are no ratings, there is no popularity contest.
So choose your tools appropriately and let everyone know and we can then start talking about what you made with your tools.
Please ask if you have any follow-up questions, and welcome to Pixelation.