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I think it drops regardless if you wait for the loot drop screen or not. Crota's End is odd in that it doesn't show the exotic drops in the upper right corner when you get it but it WILL show in the lower left corner where it posts all drops for everyone. Happened to me last week. The only thing that posted for me when i looked in the upper corner was 2 shards but someone congratulated me for getting the Gjallarhorn. I was like... "umm no? I just got 2 shards". He told me it posted in the bottom left and that i just need to check my inventory when we got to orbit. He was right. I had the Gjallarhorn in my inventory and no we didn't wait for the raid to auto orbit. We just went straight to orbit. So next time just watch the item postings on the bottom left of the screen to see what you got instead of the upper right.
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That happened to me yesterday. We were just messing around after we finished trying to figure out who needed to run it again for one of their alternates and when we finally went to orbit was right when the screen was coming up and I got No Land Beyond. Not the greatest drop, but still an Exotic.