The reason the merge point of Indy is outside the temple is a combination of fire code and WDI. When we first did it (dusting off some cobwebs here) I want to say merge was either Station Gate and then moved to Rotunda or maybe started at Rotunda. I know it was at Rotunda because of DOSH's safety film requirement... but I can't remember if they were testing Fastpass before or after the film modification (since it all kind of came flooding downhill at the same time).
Here's the basic story. Merge for Wheelchairs, VIP, and Fastpass was at Rotunda. Because of this the exit tunnel was blocked with a combination of wheelchairs, movie stars, and fastpass holders. The Fire Marshell came down hard on it, we closed shop. We then suggested that Merge be moved to entrance of Bat Cave because it is a common "line cut" point anyways. We figured it would "kill two birds with one stone" . People aren't dumb enough to cut the line with a CM standing there, and the next "choke point" is at the top of Bamboo Canyon so we had plenty of wiggle room to skate the code.
WDI... WDI said "no" because they wanted the merge point outside. They wanted people to "walk through the line and be fully immersed in Disney theme instead of stuck standing in line staring at the walls out of boredom". So... ummmm... yeah... that was WDI's brilliant creative move. Thanks to them we had to re-drill Digs, re-drill marquee entrance. Even with the additional queue space Indy still uses a modified crossover to use Jungle's boathouse on busy days. And guess what... people get past Merge and go running through the temple completely ignoring the intricate theme. Then to add insult to injury, those who exit sometimes cut the line and get right back in at the Bat Cave... meanwhile everyone is standing around outside for the majority of their 75 to 90 minutes.