I have several projects with 1000-2000 tasks. When I update, it's only the current campaign, so I only need 100-200 tasks to be visible, not the historical ones that are 2+ years old.
I am not sure which feature is the Timeline Planning Mode, possibly the gantt chart? If this is the gantt chart then you should be able to still apply filters on this screen. If this is not the correct area please let me know which feature you are using and I can take a look at it.
In the Timeline Planning, all filters/views/groupings are removed. I understand the intention and that it makes the updates faster, but at least the option for "incomplete tasks" would make this feature beneficial on larger projects.