I feel your frustration but (respectfully) I don't agree with @Sozap's assessment here. Although I have used it in a lossless pipeline - which is .png in and .png out as image sequences, that's about as a lossless (and
as storage heavy) as it gets.
However, it's entirely possible to get very high-quality video out of Natron provided you put high-quality video into it in the first place. The trick is knowing how to use the encoder options which are pretty vast
In fact, Natron is quite capable of outputting completely uncompressed video in a number of intermediate formats, such as Apple ProRes 4:4:4 and better still, it can set most of it up just by setting the correct container in your Write node.
When you drop a writer node in, simply select .mov (or enter a filename with .mov and it's detected automatically) and presto, Natron sets you up with (at least in my 2.2 release) Apple ProRes 4:4:4. This feature seems partly broken for .mp4 right now, but you can still access the settings (and the compression levels) by rolling down the settings as shown here.
The section here shows a fake spotlight effect (vignette) which has been output using Natron ProRes 4:2:2 as a digital intermediate and then further processed and re-compressed to .mp4 using Kdenlive. Now this isn't going to win an Oscar for quality, the entire 80 minute (@720p) performance is under 300Mb in size and quite acceptable in terms of visual quality.
Just to compound matters further, the original footage was shot on a Canon 600D in very poor lighting conditions and rendered out to an SD card as a 4:2.0 H.264 compressed file! So this final image has been compressed not once, but twice!