Hey there! Thanks for reaching out! I'm honestly not sure on what's going on with your theme 🤔 everything is seted up on the theme.xml as it should, however here's a few things I can suggest you trying to hopefully fix this!
1. First make sure the Screen Scaling and UI Element Scaling are set to 100%, UI Element Scaling can be set to 200% if you're on a high resolution such as 4k
2. While I was making the theme I noticed that sometimes the theme doesn't fully update until you: Change the theme > Close Aseprite > Reopen Aseprite. So in case you haven't tried that yet, give it a shot!
3. I notice you're using "Aseprite v1.3-dev" which is a bit behind on the version I based this theme around "Aseprite v1.3.9.2" I'm not sure how much they've changed about themes from 1.3 to 1.3.9.2, so that could be a reason too, therefore try updating Aseprite to the newest version
I double checked rn that the Theme.xml file that I uploaded contains the correct measurements for the bars and it does! I can notice that some measurements are working on the screenshot you shared because the color buttons on the bottom left are sized properly, the elements inside the timeline are sized correctly as well as the tab size
These are the only reasons I can think of that could be messing with the context bar and the timeline buttons, Aseprite theme creation is a bit limited and still developing more and more so it might be the case that the version you're using might be the problem, regardless option 2 might do the trick, fingers crossed!
I really hope any of these managed to solve your problem! if you do please share with me what made the trick <3 could help me make the theme page more informative