Arrows overlap atoms of chemical elements after save/load to/from RDF or layout actions

**Steps to Reproduce**
1. Add reactions with chemical elements containing atoms:
[overlapping-issue.zip](https://github.com/user-attachments/files/17523417/overlapping-issue.zip)
2. Make Layout or save/load to/from RDF actions

**Actual behavior**
- Arrows overlap atoms of chemical elements:

**Expected behavior**
- They are not overlapped, expected indent should be clarified - TBD

**Environment details:**
- Reproduced on RC SA env;
- Ketcher [Version 2.26.0-rc.6] Build at 2024-10-25; 09:57:12;
- Indigo Version 1.25.0-rc.4.0-g8862ccb7e-wasm32-wasm-clang-19.0.0
- Desktop, Windows 11 Enterprise
- Chrome, Version 130.0.6723.70 (Official Build) (64-bit)

**Additional context**
- Test case is added to xls and have to be automated after fix
- The defect is detected during retesting of https://github.com/epam/Indigo/issues/2555, but initially it's related to https://github.com/epam/Indigo/issues/2309