I agree with @Hal_Al in that your attempt in reading and quoting a portion of worksheet 3 are not your facts.
The IRS, in general, do a pretty good job at explaining the code and regulations in the publications. However, when the situations get complicated, as is this one, sometimes they are not the model of clarity, but that is their attempt at trying to put into english, Treasury code and regulations and technicalities within the language of each.
The section you are reading is saying that if there was some non qualified use during your last 5 years of ownership beginning AFTER the last date this was considered your principal residence, that time would not be considered non qualified.
By way of example, if you used the home as your principal residence beginning 1/1/ 2014 up until 1/1/2019, moved out and sold it in 2020, 2019 and 2020 would not be considered non qualified use even though you were not using it as your principal residence.
As to your main overriding question on IRS "behavior" if something in a publication may be confusing or misunderstood and you followed what you believe to be accurate based on the publication, you will not prevail if audited, if you go to IRS Appeals, if you go to Tax Court or some other Court. You may not be subject to any penalty, but you will still owe any tax and interest.
*A reminder that posts in a forum such as this do not constitute tax advice.
Also keep in mind the date of replies, as tax law changes.
