I am working on this even as we speak :)
Until that lands, you might be able to use a location-block in your nginx configuration if you structure your URLs so amp gets served out of its own directory or something. Then you can turn off a few filters in that location block. Based on my initial work, that set includes:
add_instrumentation
prioritize_critical_css
dedup_inlined_images
defer_iframe
delay_images
insert_ga
javascript_filter
combine_javascript
defer_javascript
inline_javascript
outline_javascript
lazyload_images
local_storage_cache
make_show_ads_async
As well as:
pagespeed CriticalImagesBeaconEnabled off;
Also -- can you send a pointer to the automatic AMP converter by'automatic'? Searching for 'amp automatic converter' gives all kinds of totally unrelated hits :)
-Josh