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AME is basically the default engine for PrPro's exporting. Setting your export settings in PrPro uses presets from AME, so if you've made some for specific repeated jobs ... you would just choose that preset in PrPro and "go". Queuing over to AME allows you to use the full range of options for each format/codec, not just the presets.
I'll let someone else answer about Ae ...
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Also, rendering in AME means you can keep working in PP while it works in the background. This can save a ton of time when you're stacking jobs.
i have never experienced any anomalies in any direct ae renders
that said, media encoder is much more flexible in configuration options
i will normally render ae comps via dynamic linked premiere timelines,
queued to media encoder
queue vs. direct render:
there should be nought difference in quality,
and negligible difference in encoding time
i normally queue, if only for the convenience of
multiple exports from a session in one shot
It's all about time management.
You can also save the lengthy, time consuming renders to run at the end of the day, leaving more working hours to perform edits.
As Snarky points out, you can render one file to several flavors (such as rendering an online, HD and archive resolutions in one go).
Create watch folders attached to specific encoding recipes to automate conversions, or for trans-coding for manual ingest as an alternative to Prelude.
As I shoot and fill a card/drive, I'll drop the contents into a watch folder and let it transcode as I continue to shoot on another.
I have found default settings in Premiere Pro directly utilize all cores on the system and their processing power, whereas Media encoder used sometimes only 25%, and only one core at 100%; However this can be changed by inserting a Settings.ini file into the executable folders of Adobe Premiere, After Effects and Media encoder with the proper commands; and has increased my core and thread utilization in Adobe Media Encoder to the maximum extent... as is the same for After Effects, Premiere Pro! For instructions on this simply search for the youtube video ""Render 300X FASTER | Premiere / After Effects / Media Encoder"
Interesting comments. I'll look at that link later.
AME has always used the full resources of my system when it could. I don't believe your experience is normal.