I still can't reproduce this. This time I tested on an iPhone 5S running iOS 10.1.1. It resumed fine every time. I found that if you press Home then Safari again really quickly, the audio doesn't stop at all, it seems like that doesn't count as actually leaving Safari. If you press home then wait for the audio to stop, then it seems to actually have suspended Safari and then resumes if you tap Safari again. Sometimes it takes a moment and the screen is blank until it resumes. Even if I press Home again while the screen is blank and it's waiting to resume, and keep going back and forth like that switching when it's trying to resume, I hear a tiny clip of audio as it presumably resumes and immediately pauses again. If I leave it showing Safari, it always comes back and resumes playing the audio.
I'm using the .capx in the original post and preview-over-wifi if that makes a difference.
I've tested both an iPad and an iPhone now and I honestly can't reproduce any kind of problem at all. As long as this is the case there is nothing I can do. Perhaps you would have more luck if you file a bug directly with Apple about this at https://bugs.webkit.org/. Even if I could reproduce the problem, given it works on other browsers, it seems likely it's an iOS/Safari bug anyway - in which case reporting it directly is just what I'd have done myself.