Here is where I think the confusion lies on both of our ends. The verbiage and explanations are a bit convoluted.
From your article - For IRA distribution purposes, all IRAs (except Roth IRAs) are considered one big giant IRA. It doesn’t matter if you have one IRA that was rolled over from a former employer, and one SEP IRA with your current employer, and one contributory IRA where you put annual contributions, and one after-tax IRA where you put contributions for which you do not take a deduction. All four IRAs will be considered one IRA any time you take a distribution. (***Note he does not include Roth accounts in this last two sentences in that paragraph setting the stage for the rest of the article***)
What this says to me and what my understanding has always been - When you take any distribution - conversion or otherwise - the Pro-Rata rule applies to all IRAs except the Roths as they are a different animal. (Whether you have both pre and post tax IRA, or 100% in either - Pro-Rata is applied) If you take income for spending or a distribution to do a conversion - the Pro-Rata rules apply so if you have pre-tax and post tax dollars in various IRA's then you must take distributions in the same proportion, regardless of which account the funds reside. If you only have type of funds then the Pro-Rata application is 100% either way.
The Roth stands separate and alone from that discussion.
In thinking through practical applications - In your case you did a Roth Conversion under the special provision for a 4-year tax spread. If I think through that - many people who only had pre-tax IRA's took advantage of that.....meaning 100% of the distributions turned into a Roth conversion would be taxable now (or over 4 years under that special provision).
No one would have done that if the outcome would be that they converted 100% pre-tax funds to a Roth (with Pro-Rata rules requiring taxes on 100%) - when the outcome would be that down the road then those same Roth dollars are taxed at the 100% Pro-Rata level as well. It would defeat the purpose of any pre-tax Roth conversions and cause double taxation.
I think there are a lot of poorly worded illustrations on the Pro-Rata rules - and they do not properly address that Roth accounts stand unique and separate from the Pro-Rata rule. Pro-Rata is for tax computations, and as designed, the Roth allows for tax free withdrawals after 59 1/2 / 5 years so that calculation doesn't even come into the discussion.
I'm always interested in being corrected if one of our CPA's will chime in.