I just got off a call with Apple Support, and they seem interested in this issue - I've got another call setup for tomorrow and we're going to to do some back-and-forth diagnostics on this to see what is actually causing the issue, and the rep says he sent it on up the chain because it was unusual but important that it get noticed. I've taken some notes regarding the issue and I'm posting them below, and I will keep this thread up to date as things progress.
Apple Case #683680964
Support Forum: https://discussions.apple.com/thread/6563016
Issue: iPhone 6+ battery drains rapidly and Safari always shows as top spot in battery usage for both 24h and 7d, usually over 40%.
Before: Used Safari on iPhone 5S and enabled Settings>iCloud>Safari, along with installing iCloud for Windows on Desktop, Laptop, and Surface Pro3, all of which had enabled "Sync bookmarks with Internet Explorer". Normal battery consumption, but no detailed usage info available.
Change: After purchasing iPhone 6+, initially looked similar and got 30+ hours of normal usage on device from a full charge. After 2-3 charge cycles, began noticing severe battery impact, cannot go 24h without recharging and the usage (standby) is always the same as usage (in use). Safari began showing up at the top of the usage list, generally over 40% usage. No changes were made on iCloud for Windows, no other devices were changed. Noticed that while Safari is open, the data usage icon would briefly appear every 1-2 seconds in the status bar, possibly indicating recurring usage while the app is inactive? Icon does not appear on the home screen despite apparent Safari battery drain.
Prior to call - Uninstalled iCloud for Windows and all associated Apple software on Laptop and Surface Pro 3, ran Apple Software Update on Desktop but no updates available, ran Windows Update and installed all available updates and rebooted. No changes made to iCloud for Windows on the Desktop, no changes made to iPhone 6+. Noticed that data usage still appears every 1-2 seconds with Safari open, apparent behavior unchanged.
After Call 10/22 16:35 - On iPhone 6+, disabled Settings>iCloud>Safari, selected "Keep on device". Recharged to 100% and then unplugged, followed normal usage patterns. Followup call scheduled for 10/23 16:00.