Agree with this. They are re-solving a problem that has been solved better by others before (with R-trees).
They may well be using some data storage where spatial indexing is not possible or standard. Geoparquet is a common one now - a great format in many ways but spatial indexing isnt there.
Postgres may be out of fashion but still an old fashioned postgis server is the simplest solution sometimes.
Why do you consider Postgres + PostGIS out of fashion? What are people using for spatial data these days?
I wouldn't say R-trees solve the problem better. Joining multiple spatial dataset indexed with r-trees is more complex as the nodes are dynamic and data dependent. Neighborhood search is also more complicated because parent nodes overlap.