doc: Various fixes

[dweindl]

• Replace references to private functions
• Fix some typos and formatting

Closes #3062.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.58%. Comparing base (d1de05d) to head (61099e4).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3102      +/-   ##
==========================================
- Coverage   78.32%   77.58%   -0.75%     
==========================================
  Files         315      315              
  Lines       20466    20464       -2     
  Branches     1500     1498       -2     
==========================================
- Hits        16030    15876     -154     
- Misses       4427     4579     +152     
  Partials        9        9              

Flag	Coverage Δ
cpp	71.72% <100.00%> (-0.09%)	⬇️
cpp_python	37.73% <50.00%> (+<0.01%)	⬆️
petab	46.46% <75.00%> (+<0.01%)	⬆️
petab_sciml	13.79% <25.00%> (+<0.01%)	⬆️
python	70.36% <100.00%> (-0.09%)	⬇️
sbmlsuite-jax	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
include/amici/model.h	78.04% <ø> (ø)
include/amici/solver.h	100.00% <ø> (ø)
python/sdist/amici/_symbolic/de_model.py	91.86% <ø> (ø)
python/sdist/amici/exporters/sundials/de_export.py	96.38% <ø> (ø)
python/sdist/amici/importers/antimony/__init__.py	83.33% <100.00%> (ø)
python/sdist/amici/importers/bngl/__init__.py	100.00% <100.00%> (ø)
...hon/sdist/amici/importers/petab/_petab_importer.py	86.78% <100.00%> (ø)
...thon/sdist/amici/importers/petab/v1/sbml_import.py	97.75% <ø> (ø)
python/sdist/amici/importers/pysb/__init__.py	94.64% <ø> (ø)
python/sdist/amici/importers/sbml/__init__.py	82.40% <ø> (-11.93%)	⬇️
... and 2 more

... and 7 files with indirect coverage changes

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