The part that there is missing geometry is the part that has no sketch or anything like that above or on the cut out.
If you look how I did the cutouts It's with the sketch that makes the body.
There is a few reasons I do it that way.
1) it's super hard to accidentally move that part of the sketch.
2) It's very easy to change the sketch and add to it.
3) I have found the model is more stable.
The reasion for 1 is if you move the body's sketch or the cutouts sketch by accident you get the yellow warnings or a complete fail.
The reasion for 2 is diamention and constraints placed at the correct spot lock it down and if you wont to move a line's positions you just use the dimensions to do it and if the constraints are doing there job and are placed at the correct spots the sketches move in a predictable way.
For 3 it's if you have other elements attached to a stable component, body or sketch, when you change that what ever it will move together.
Also it's one sketch 3 extrudes it's a tiny file.
I do cabinet making the same way not very many sketches but lots of extrudes, patterns and move/copies it's very stable this way with a object that I can changes on the fly with next to no fails and it may be one constraint or a diamention put in the wrong places, I fix it and it's all good.
My steps to do it was just ruff in the sketches, do the constraints then dimension it, do the extrude for the outside profile do the extrude for the inside bottom of the body then I just extrude/cut the cuts outs, tested the model to make sure it was stable and exported it out and posted it.
Just haveing sketches placed here or there and just doing it that way as you are not sure that is where you wont the sketch to be, can work and should work, I give you that one here's my but on that.
If you move the body what will happen to the sketches if they are now on the wrong plane or are being used in the body, the answer is something i never wont to know, it will be yellow and red flags. so I just don't go there. It can be by accident.
You can fix it when it first goes yellow or red by redefining the sketch plane then useing constraints and dimensions to lock it down or just redo it.
if you leave it be and carry on it will get worse as what happened to your file it just died.
We know there are problems with fusion and if you do stuff one way it can be bad.
So to make things easier for noobs to fusion, we have this forum I was a noob 2 years ago, I made big mistakes one of the fusion staff did a screencast for me that put me on track, then I need to know how to do something else, I asked one of the EE and he said how to do it, I still do it the same way and he still is a EE.
You can still do it the way you are doing it, it should work ( I would not do it that way myself) but as soon as a yellow warning pops up stop and fix it, if something has move redefine sketch if you cant fix it jump on the forum and post the file or a screencast and a description of what you wont to do.
if redefining the sketch fixes it carry on then.
Now to you know lots about programming that's cool, but this is cad/cam thinking about it as a coder it wont help you at all, there is quite a lot of computer guys here and in the end it's a cad/cam program that you can help evolve with add ons and that sort of things in the api. I am not haveing a go it's something I see all the time computer dudes rageing that they know all about programming and it should do this or that and they have a hard time working with fusion until they just let it go and do it the fusion way.
The vids you have to be careful A lot of them are out of date now anything from the start of 2016, may be wrong, 2015 a high chances it's out of date.
I don't work for ADSK I am just a user, ANd there is no attack on you from me, it's me saying what I see and only that.
And I will help you if you need it or wont it.
