Example of how 2 sets of coordinates (in the same projection) can be compared for proximity.

buffer_compare.R

# Buffer the coordinates with a desired distance
sp.espoo.etrs89.buffer <- gBuffer(sp.espoo.etrs89, byid=TRUE, width=100)
sp.espoo.etrs89.buffer <- SpatialPolygonsDataFrame(sp.espoo.etrs89.buffer,
                                                   sp.espoo.etrs89@data)

sp.tarto.etrs89.buffer <- gBuffer(sp.tarto.etrs89, byid=TRUE, width=100)
sp.tarto.etrs89.buffer <- SpatialPolygonsDataFrame(sp.tarto.etrs89.buffer,
                                                   sp.tarto.etrs89@data)

# See which SpatialPoints from the KML files fall within the buffer from sp
# points
espoo.buffers.with.kml.point <- sp::over(kml.espoo.etrs89, sp.espoo.etrs89.buffer)