I'm not sure how using a grid system or something like bootstrap is "pushing presentation into markup".
Regardless of whether you use bootstrap or not you are always going to be specifying CSS classes which describe the presentation of elements, not sure how else it can be done?
Screen reader software will generally ignore anything that it doesn't understand or deem irrelevant.
Whenever I have tried screen readers they will say "ok, there's 3 divs with content here. Let's read them out one at a time or just read the headings and wait for the user to select one". How they are arranged in a grid will be irrelevant to the software.
Does bootstrap present some particular problem for screen readers?
You are yet to explain what you think best practices should be here.