Song is not marked as modified when changing various options

### System Information

Linux 7.0.3-arch1-1 #1 SMP PREEMPT_DYNAMIC Thu, 30 Apr 2026 18:41:12 +0000 x86_64 GNU/Linux

### LMMS Version(s)

1.3.0-alpha.1.976+3b4b54c

### Most Recent Working Version

_No response_

### Bug Summary

There are many options which do not mark the project as modified when messed with:
- the "top bar" options of the project: tempo, time signature, master volume and global transposition;
- changing ~~song editor options such as zoom~~ piano roll key/scale, which are now saved per-project as of #7854;
- changing the values in knobs;

### Expected Behaviour

I believe these should be marked as modified when messed with, with the exception of being changed when automated (I'm not fully sure how it should work in that case).

### Steps To Reproduce

(Not relevant)

### Logs

(Not relevant)

### Screenshots / Minimum Reproducible Project

Here is an example with the "top bar" options.

https://github.com/user-attachments/assets/b5a6fa67-ff01-4a4f-a477-7217ad34249f

### Please search the issue tracker for existing bug reports before submitting your own.

- [x] I have searched all existing issues and confirmed that this is not a duplicate.

Start by reproducing the missing modified-state behavior with the top-bar options, piano-roll key/scale settings, and knob values, then trace how project changes are marked. Done means the listed manual changes mark the song as modified while automated changes follow an explicitly decided behavior.

Written by the indexing model from the issue text.