It’s just that in your graphic, your HOURS column has the hour hand pointing to 12:00 in every row, but in your MINS and SECS columns, the hands point to every 5 minute interval. Shouldn’t the HOUR column have just the hour hand pointing to every 5 minute interval (i.e. every hour)? If you did that, you’d have all of the elements for the layered approach.
You’d also need a special firmware that redraws the clock every 5 seconds based on the real-time clock chip. Currently sequencing of animation frames (and between animation folders) is handled by the much less accurate internal Arduino clock (millis function). If you’re making a clock, you definitely want to tie into the RTC chip. I’d be happy to help with this.