More consistently use existing charge caching

[mattwthompson]

Description

A few code paths didn't use the improvements of #1066 / #1069, which caused some horrible performance in some number of corner cases. (Writing out GROMACS files in the protein-ligand example took 10 minutes (!) compared to a few seconds for OpenMM.)

I'm more than a little confused as to how from_openmm code paths might have been hit in this example - which just uses SMIRNOFF force fields and Interchange.combine - but I could be misremembering which changes actually affected things.

Checklist

• Add tests
• Lint
• Update docstrings

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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.39%. Comparing base (dec585e) to head (396d472).

Additional details and impacted files

---- 🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[mattwthompson]

Upstream:

============================= slowest 20 durations =============================
474.12s call     examples/protein_ligand/protein_ligand.ipynb::Cell 20
427.49s call     examples/protein_ligand/protein_ligand.ipynb::Cell 22
188.02s call     examples/protein_ligand/protein_ligand.ipynb::Cell 26
95.74s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 14
85.04s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 18
69.02s call     examples/packed_box/packed_box.ipynb::Cell 6
65.37s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 8
62.18s call     examples/protein_ligand/protein_ligand.ipynb::Cell 7
59.11s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 6
32.89s call     examples/lammps/lammps.ipynb::Cell 6
30.41s call     examples/amber/amber.ipynb::Cell 4
30.02s call     examples/host-guest/host_guest.ipynb::Cell 6
27.48s call     examples/protein_ligand/protein_ligand.ipynb::Cell 9
20.64s call     examples/openmm/openmm.ipynb::Cell 5
19.13s call     examples/protein_ligand/protein_ligand.ipynb::Cell 18
18.69s call     examples/openmm/openmm.ipynb::Cell 4
14.53s call     examples/packed_box/packed_box.ipynb::Cell 4
14.51s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 19
12.16s call     examples/openmm/openmm.ipynb::Cell 0
11.10s call     examples/amber/amber.ipynb::Cell 0
================= 119 passed, 3 skipped in 1247.79s (0:20:47) ==================

These changes:

============================= slowest 20 durations =============================
89.78s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 14
64.33s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 18
63.69s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 8
63.53s call     examples/protein_ligand/protein_ligand.ipynb::Cell 7
57.87s call     examples/ligand_in_water/ligand_in_water.ipynb::Cell 6
38.[25](https://github.com/openforcefield/openff-interchange/actions/runs/11958262648/job/33337380981?pr=1115#step:8:26)s call     examples/packed_box/packed_box.ipynb::Cell 6
33.39s call     examples/lammps/lammps.ipynb::Cell 6
30.02s call     examples/host-guest/host_guest.ipynb::Cell 6
29.95s call     examples/protein_ligand/protein_ligand.ipynb::Cell 22
28.00s call     examples/amber/amber.ipynb::Cell 4
[26](https://github.com/openforcefield/openff-interchange/actions/runs/11958262648/job/33337380981?pr=1115#step:8:27).46s call     examples/protein_ligand/protein_ligand.ipynb::Cell 9
25.93s call     examples/protein_ligand/protein_ligand.ipynb::Cell 26
21.18s call     examples/openmm/openmm.ipynb::Cell 5
19.35s call     examples/openmm/openmm.ipynb::Cell 4
17.60s call     examples/protein_ligand/protein_ligand.ipynb::Cell 18
15.10s call     examples/packed_box/packed_box.ipynb::Cell 4
11.91s call     examples/openmm/openmm.ipynb::Cell 0
11.38s call     examples/lammps/lammps.ipynb::Cell 0
11.18s call     examples/amber/amber.ipynb::Cell 0
9.00s call     examples/packed_box/packed_box.ipynb::Cell 2
================== 119 passed, 3 skipped in 304.15s (0:05:04) ==================