`model2netcdf.ED2()`—Fix dimension issues when PFTs missing from ED2 output (Follow up on #3140)

[Aariq]

Description

Apparently https://github.com/PecanProject/pecan/pull/3140 didn't fix this bug entirely. If a PFT is missing from the ED2 output for a full year, then there were still problems with the dimensions. Instead of using the ED2 output to figure out what PFTs need to have NAs for the output, this PR changes it to use the PFTs supplied by the user (e.g. in settings).

Motivation and Context

Review Time Estimate

• [x] Immediately
• [ ] Within one week
• [ ] When possible

Types of changes

• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• [ ] My change requires a change to the documentation.
• [x] My name is in the list of CITATION.cff
• [ ] I have updated the CHANGELOG.md.
• [ ] I have updated the documentation accordingly.
• [x] I have read the CONTRIBUTING document.
• [ ] I have added tests to cover my changes.
• [ ] All new and existing tests passed.