Sadly there are lots of routes that journey planners will suggest which don’t necessarily take account of programmed interchanges. There are no direct trains between Euston NR and St Pancras NR, and as someone making that transition would need to use two OSIs with plenty of internal walking, I imagine that it was requested by ATOC in the run up to Oyster extending to all NR routes. They also requested Marylebone NR to Paddington NR which is almost never used. There are also no direct trains between Aldgate and Aldgate East unless you count a Circle line train which turns into a District or Ham&City train at Edgware Road.
Finally, Richmond to Clapham Junction is quite frequent and some of the services are limited stop, Clapham Junction to East Croydon has plenty of non-stop services, so I’m not surprised that the route sometimes turns out to be quicker.