I worry you're right. It'd be a shame not to have the convenience of getting the job done in Media Encoder. The thought of having to encode twice is really repelling. These aren't esoteric file types now that we're talking about accommodating major browsers for the sake of HTML5 video.
Adobe people, I hope you're listening.
>Adobe people, I hope you're listening.
Feature Request https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform
Adobe knows that web content developers want WebM and OGV (and of course also MKV) support... But they are definetely NOT listening, because (due to the decision to drop WebM support as they promised) they've now actively decided to wage war against HTML5 video!
Most likely they have already received thousands of requests for MKV, OGV and WebM support for the past 3-4 years.
But Adobe is by no means interested in competition from the open source containers and the community formats, so they are doing whatever they can to stop it by only supporting commerical (license encumbered formats) in their hegemonic Flash Player.
I guess we ought to stop Adobe then...
Have you filed the Feature Request yet?
Adobe does listen to the users. Now, it could well be that there are not yet enough voices for them to commit $ to the development and implementation, so their lack of action might well be a reflection of not enough requests, such as MKV support.
When the voices reach a tipping-point, that Adobe can use to justify the implementation, I am sure that it will happen.
Adobe support for webm and others is not likely. Firefox is the only one of the four browsers I checked that does not support HTML5 mp4 videos. The other three are Chrome, IE Explorer, and Safari.
Mozilla, as a non profit, has problems with licensing fees.
Mozilla claims they do support webm. So I found a webm converter at "Micro Video Converter": http://www.mirovideoconverter.com/.
The downside is the webm files, in addition to taking time to convert, are twice the size of mp4 files and, while I can get the files to play locally, they don't play on remote web server.
Going forward I'll place a note: "Current revisions of Chrome, IE Explorer and Safari support HTML5 video frames embedding mp4 files. Mozilla Firefox does not support mp4 video." beneath the video.
I use XMedia Recode to create my WebM version for Firefox users. While I don't agree with Mozilla's stand on this one, it is the best browser out there and I don't want folks visiting my site to have to use something else.
I just spent a couple hours trying to download the XMedia Recode. All the download spots have objectionable adware blocked by my firewall. If Mozilla really cared about their H.264 stance they would make it easy to download a converter for occasional developers.