So, I need to use formLayout as top level, because it's a requirement to run Process Model, but, i have a Header Content Layout (where I can't reproduce using another layout), and when I try to use this as formLayout child, there a error message that is not possible, because is not compatible. What can I do?
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The formLayout is a shortcut, but you should be able to duplicate all you need with other components. You can still get sections and anything else you need inside the contents:, and at the bottom you can just include a buttonArrayLayout. You can use columns or a side-by-side to get Cancel on one side and Submit on the other, and they can all be configured to submit, or startProcess, or you can attach a!startProcessLink to other components or attach recordActions anywhere in the form. And the form header can be duplicated with rich text or left out.
In most projects I never see anyone using formLayout on any of their forms anymore. Perhaps you could elaborate on your requirement to "run Process Model" unless this answer is sufficient.
I think the only things you lose if you don't have a form layout are form-level validations and button formats on mobile. Personally I agree with Dave - these are not that important in most cases (and you can still mostly achieve the same behavior using section level validations and button array layouts respectively).