I mean what makes it more acceptable is that you have HMR and instant preview during development. So, all the transformations and bundling aside, you do see how it runs during development.
However I have been in a few situations at work where all of a sudden we did have issues that required us to dig deeper. There were also some bundling related issues that caused problems in production deployments. At that point many co workers had no idea how to even approach it to be honest.
I've had similar experiences with compiled languages in one form or another throughout my career as well. I don't think JavaScript is particularly special that we need to call it out for things like TypeScript, minification, or bundling.