That part of the flow chart does appear to be confusing, but here's what they intended and why it makes sense:
There are some transactions and types of collateral which will be covered by Revised Article 9 (RA9) which were not covered under Old Article 9 (OA9). For example, commercial tort claims are a new category of collateral under RA9. Let's say you were a lender who had made a loan secured by a commercial tort claim prior to RA9. You would have had to perfect, if at all, outside Article 9, since OA9 didn't cover that type of collateral, but let's say that for whatever reason you didn't actually take steps to perfect. Then let's take a situation where the lender's security interest SHOULD have been perfected under old Article 9, but the lender, for whatever reason, didn't actually perfect it under old Article 9.
In either of these instances, when using the flow chart, you would answer "No" to the question of whether your security interest was perfected under Old Article 9 or outside Old Article 9. If you had not perfected under or outside OA9, you would need to take steps under RA9 to perfect before July 1, 2001 (or whatever date the Revision becomes effective on in the applicable state, since some states have nonuniform effective dates). Or, if circumstances were different and you HAD either perfected under OA9 or outside OA9, you would answer "Yes" on the flow chart.