The only AppStore player claiming to use AC3 is CineXPlayer but as you have said they don't have native iPhone 5 res yet and I'm not 100% that it supports MKV.
1. Isn't there any way of enabling UPnP or SMB instead of / in addition to FTP? Then, you could be able to use e.g. CineXPlayer (with UPnP).
2. CineXPlayer doesn't support FTP (see above), only UPnP. The currently available iPhone version (2.8.2) does play MKV's but in software only and isn't really recommended for playback. You could drop a line to the dev (he's here: https://forums.macrumors.com/threads/1478727/ ) so that he speeds up releasing the much superior (but in no way flawless) 3.x series for the iPhone as well.
3. I don't have any good news for you. The AppStore players that do support FTP (VM Player, AcePlayer, Oplayer, eXPlayer, BUZZ Player, GoodPlayer, eXPlayer) have all removed AC3 support. (In addition, only one of them, eXPlayer, supports hardware-assisted playback of iOS-native files.)
4. The jailbreak-only XBMC supports FTP streaming (along with AC3 / HW acceleration, even with MKV files) just fine - but you'd need JB...
5. Note that the, assuming you've downloaded it to your target device before it being censored out of AppStore, in the AppStore still available AVplayer does support AC3 but has no streaming support at all. This means you can only download files, not stream them.
All in all, the situation is pretty dire, "thanks" to Dolby and Apple - they've successfully destroyed the platform as a viable, great, flexible, all-in-one multimedia playback platform with their absolutely silly AppStore rules (Apple's not allowing HW acceleration with non-native containers) and (Dolby's) greed. It'd be the best if you converted your video files - adding an additional AAC track is very easy with tools like MKVTools. (Need the URL of my dedicated tutorial?) Also, you really should consider switching to an iOS-native container and using UPnP or SMB so that you can have hardware acceleration.
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