A couple quick comments (though this is probably a mostly dead topic by now)…
The original question mentioned workflow in the subject. SU does not prescribe a workflow any more than MS Word or Excel does. They are all just tools, though very powerful & complex ones. A hammer or screwdriver does not prescribe the workflow for how to build a house or a cabinet. This is a useful comparison, because the workflow for building a house would be quite different than that for building a cabinet. And SU can be used for either (and many more things). One of the fertile topics of conversation both in the forums & in the videos is the various workflows that people have worked out in their various contexts.
As for additive or subtractive modeling, it really depends on what you’re making. I use both.
Don’t miss the importance of components and groups. When you watch the videos, you may get the impression that these are just more tools at your disposal. I would say that these are required elements. You can do a lot of modeling without ever drawing a circle, but you can’t do much without a component. If in doubt about which to use, make it a component, for the reasons given above. I rarely use groups - usually when I want to combine a set of components into a larger structure that will never by copied.
Layers - I have watched videos about this and read many posts in this forum about layers and so far have found no compelling reason to start using them. As mentioned above, it’s primarily about visibility - or to put it differently, it’s about how you want to present your model to others. If you are a professional architect / designer, you may find layers indispensable. If this is just your hobby (as it is mine), you may find that using scenes gets you everything you need for visibility and layers are unneeded.
Layout - I haven’t yet found occasion to use this. Depends on what you’re doing. I suspect that layout will be more useful when designing a building than when designing a cabinet. (Correct me, if I’m wrong.)
Intuition - this comes from experience. Like you, I was initially frustrated at a UI that seemed so intuitive up to a point and then suddenly became inscrutable when stuff didn’t work out the way I wanted. I have had to develop new intuitions about how to work with SU, which has come with much practice and much reading what the sages write in response to these forum posts. For sure, they have developed a unique way of looking at problems that often surprises me.
Because many years ago I studied a little of computer graphics, I know some of the lingo & the concepts (eg. What is an extrusion?). It seems like the SU developers had that as a background. But then they had lots of interactions with architects and designers, which has shaped the way that more advanced features were developed. So those things may be much more intuitive for people with that training than it is for me.
One kind of intuition you will need to develop has to do with working around SU’s limitations. It is a very powerful & useful program. But it still has limitations. You pick this up when you read about scaling things up to make some edit then scaling it back down again. Or about only modeling the detail on a portion of your model and not maintaining the same level of detail throughout.
I once had an idea for a community. I started with a basic apartment block & some retail space at the end. I wanted to give it a certain style, so the facade had a good bit of detail. I copied these ‘modules’ to make city blocks, then copied those blocks to create neighborhoods around a central community gathering point. But the facade details were duplicated so many times, that SU was getting sooo sloooow rendering it all. It was unusable. From the forum I picked up the idea to take my apartment block into a separate SU file with all the facade detail maintained. Then in the overall community view, I removed that detail & replaced it with a texture to approximate it. That helped a lot, but it was still sluggish. You end up playing games like this just to get around SU’s limitations in what it can feasibly render, and that depends a lot on your machine.
So, yes, I get your confusion & frustration. If you wanted a piece of software that you could learn in a weekend & immediately become an expert, sorry… SU is way too powerful for that. But I have spent many enjoyable hours working with it over the years (since 2008). I hope you will enjoy the time you spend, as well.