[MRG] refactor _signatures_with_internal

[ctb]

Extracting this from #1891.

This PR simplifies the internal API _signatures_with_location() and its use in creating manifests.

[codecov]

Codecov Report

Merging #1896 (de55892) into latest (ffbc919) will increase coverage by 7.90%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #1896      +/-   ##
==========================================
+ Coverage   82.75%   90.65%   +7.90%     
==========================================
  Files         122       92      -30     
  Lines       13206     9001    -4205     
  Branches     1780     1779       -1     
==========================================
- Hits        10928     8160    -2768     
+ Misses       2014      577    -1437     
  Partials      264      264              

Flag	Coverage Δ
python	90.65% <100.00%> (-0.01%)	⬇️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/index/__init__.py	96.45% <100.00%> (ø)
src/sourmash/lca/lca_db.py	91.27% <100.00%> (ø)
src/sourmash/sbt.py	85.33% <100.00%> (ø)
src/sourmash/sourmash_args.py	93.50% <100.00%> (-0.04%)	⬇️
src/core/tests/test.rs
src/core/src/ffi/index/revindex.rs
src/core/src/ffi/minhash.rs
src/core/src/sketch/nodegraph.rs
src/core/tests/storage.rs
src/core/src/signature.rs
... and 24 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update ffbc919...de55892. Read the comment docs.

[ctb]

Ready for review @sourmash-bio/devs. Note this is an internal API (that is also pretty well tested ;).