converting mkv to webm without pixel errors

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I edited a video using a mask to have the middle part of the video playing and the other stuff colored in magenta. Later on I want to use a shader in Godot to key out all magenta pixels.

Unfortunately Godot only supports webm files. I edited my source video in Shotcut and exported with lossless ffv1. so far so good, capturing a snapshot in vlc shows clear borders: snapshot close up view

then I wanted to convert to webm. No matter how I do it, using an external converter, using shocut etc etc pixel errors around the borders show, where apparently transparent pixels float around:

pixel errors close up

the resolution is still the same but it won't work.

I really hope for some help to fix this, maybe exporting the video to single frames and converting them to webm works? I have no idea how to do so though.

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I have seen that there isn't very good software in terms of fast conversion of WebM files. I use a program called Wondershare Uniconverter to convert videos quickly and keep the original transparency. My only issue with this is that it only converts 1/3 of the videos length. In order to get around this issue, I open a video editor and upload an image to exist for 2/3 of the video just for it to be cut off. If you don't want to do that, you can always go ahead and buy it $69.95. The reason why I prefer this to FFmpeg is because FFmpeg takes hours and hours for loseless conversion of a two minute video.