Thanks for this feedback.
Since persistent symbols generally run across scenes/layouts, there's not a specific notion of a persistent's symbol being tied to the main timeline of any particular scene or layout. If you want to tie them together, you can do so by adding a symbol action (found alongside the properties list for the element) to play a specific timeline. Now this will be reflected on the main timeline and can be moved. It also means that you can better align items based on time when there are symbol actions; even if you need to remove it later you can use this when designing.
(Regular symbols will add a symbol action to play its main timeline by default on its parent. We just don't do this for persistent symbols since their main timeline is triggered on the first appearance and not by a particular scene.)
My recommendation would be to add vertical/horizontal guides in this case.
I believe adding a symbol action will help solve this problem. Also I do recommend previewing more on the browser-side when dealing with intricate symbol flows or multiple timelines.