docs: add clarification regarding write_crs and set_crs

[dluks]

There is some confusion around when to use write_crs versus set_crs. This adds a small note to generally prefer write_crs when CRS persistence is needed. Fixes #743

• [x] Closes #743
• [ ] Resolves all uncertainty around the initial issue(s)

One remaining nit that I would like to clarify in the documentation as well: when exactly should people use rio.set_crs() and not rio.write_crs()?