The check is correct, the text is slightly misleading. First, let me explain my rationale. Having user 63 as a Super Administrator is equally unsafe to using 62. 63 is the second ID a hacker would try, because most people do what you just did: installed the site, created a new user, made him Super Admin and demoted user 62.
Admin Tools checks if you have a Super Administrator account with a user ID of 61 or less. Since you normally have no access to those IDs, hackers don't bother with them. The warning text may be a bit misleading, but a. is applicable to the majority of sites and b. your site setup is still not very secure.
Nicholas K. Dionysopoulos
Lead Developer and Director
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