Fix benchmark collection gradient check

[dweindl]

• Fix instance vs class attribute for step sizes
• Only flatten problems where necessary

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 77.74%. Comparing base (a20447a) to head (aca37a7).
Report is 2 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #2564      +/-   ##
===========================================
- Coverage    77.76%   77.74%   -0.02%     
===========================================
  Files          325      325              
  Lines        21858    21857       -1     
  Branches      1473     1473              
===========================================
- Hits         16997    16993       -4     
- Misses        4834     4837       +3     
  Partials        27       27              

Flag	Coverage Δ
cpp	73.62% <ø> (-0.02%)	⬇️
cpp_python	34.20% <ø> (-0.01%)	⬇️
petab	37.07% <ø> (-0.01%)	⬇️
python	72.40% <ø> (-0.02%)	⬇️

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see 4 files with indirect coverage changes