Q: Does the Time-of-Day Clock have a means to manually sync at the Top-of-Hour to a contact closure?

The Reset Clock Seconds command (see page 21-6) can be executed from a macro triggered by a logic input.  

First, create the macro:

MPW 20 9201 DD 48 3 *       ; Reset Clock Seconds

Then, assign this macro to be executed when a logic input transitions from high to low:

MPW 26 0061 9201 *          ; Assign macro to Logic In 1 Hi-to-Lo

If your controller has its serial port attached to a server, a script on a server can send the command over the serial port:

MPW 48 3 *                  ; Reset Clock Seconds