It looks like rendering with transparency stopped working after 774962a

This is most likely a runtime issue - @benzoid did some careful testing with JalviewJS, stepping through all subsequent commits after 774962a to see what broke (https://issues.jalview.org/browse/JAL-4025?focusedCommentId=25553&page=com.atlassian.jira.plugin.system.issuetabpanels%3Acomment-tabpanel#comment-25553):

774962a - last fully working commit
272041b - rendering of different coloured transparent rectangles on top of each other stops working (ie only see colour for last rendered transparent rectangle).
1f2922e - rendering an image with transparency on top of an existing image stops working (ie only see transparent image).