I've gone over the schematic, and from what I can tell, you are correct. The entire purpose of the make-break switch on the 5-bank drop targets seems to be to change the parity of when the alternating relay (A relay) is ON or OFF. Nothing else seems to be affected.
So, why go to all the trouble to do this? From what I can tell, the only reason is to make it more difficult to keep track of the position of the FS relay. On this game, the FS relay always moves to the next even match number position at the start of each ball in play, so that each player starts their ball with the same lanes lit for 5000. Because of this, if a player knows the match sequence on a Gottlieb EM (it was always the same), and they make a note of the lit match number just before they start a new game, and they keep track of the number of lane light toggles, they can determine which match number will appear at the end of the game.
So, my guess is that this invisible parity change was included in the circuitry to make it more difficult to keep track of the match number. If all of the 5-bank targets happen to be down, then when the machine goes to the next ball in play, from the player's perspective the lane lights WON'T toggle even though the FS relay has stepped to the next even match number (and vice versa - the lights WILL toggle even though the FS relay hasn't moved at all). Obviously, this parity glitch will cause the player to lose track of the actual FS relay stepper position if they are counting the number of lane light toggles.
That guess may sound far-fetched, but Gottlieb (and the other companies) always had something in their circuitry to obscure the 0-9 stepper so that the match number was difficult to track. That's because, back in the day when these machines were on location, it was fairly common for players to tilt out their last ball on any game where the match number was known in advance. As soon as their score showed the correct match number, they would tilt so they could win a free game by matching. This usually occurred on machines where the 0-9 stepper was stuck, and the machine always showed the same number for match every game.
The manufacturers were well aware that no operator would want a game that let a clever player figure out things like the next match number.