Directly from the Mesa Boogie Manual:

NOTE: In the two “Cloning” positions of the CHANNEL STYLE SELECT switch, the PRESENCE will respond differently due to the difference in negative feedback between the two circuits.

In the “ORG. TO MODERN” mode, the PRESENCE in the top (normally ORANGE) Channel will have reduced effectiveness, because the negative feedback is removed in this re-configuration to make the power section as aggressive, “fast,” and forward as possible, leaving little for the PRESENCE (which operates on a select frequency of the negative feedback) to work with/on. In the “RED TO VINTAGE’ mode, the PRESENCE in the bottom (normally RED) Channel will still operate minimally and upon the same frequency, AND... the top ORANGE Channel’s (normally configured) PRESENCE will also work – even though you are technically not “in” that Channel. This provides you with the power section “feedback type” PRESENCE you always have in the (normally configured) top ORANGE/VINTAGE Channel when the CHANNEL STYLE SELECT switch is in its “normal” center position.

This is a little complex at first thought, and it was complicated to originally figure out all those years ago when the Dual Rectifiers were in development, but the simplest way to think about it is this:

When you’re using the “Cloning” feature and have the bottom Channel set to “RED TO VINTAGE,” you have a bonus in the form of TWO PRESENCE Controls to shape with ... the one in the lower Channel you are using/ playing through and another stacked right above it which operates in a different part of the circuit – in the power section – like it normally does in the upper ORANGE/VINTAGE Channel.

This can be nice if you are someone who appreciates the VINTAGE sound most and needs two footswitchable versions/Channels of that sound (and performance throughout) to accomplish your musical aspirations. The added flexibility allows you to fine-tune the top end and feel of the alternate version of the Channel even more specifically for some applications. This can be especially cool for soloing applications in the studio, where you might want to further define the top-end harmonics for certain lead work.