Try a subquery like this: we select from the results of the xmatch and then inner join. For a test mycat with a 1000 rows this query runs in less than a couple of seconds.
select match.ls_id, match.ra, match.dec, match.dered_mag_g, sdss_phot.dered_g
from (
select tractor.ls_id, CAT.ra, CAT.dec, tractor.dered_mag_g
FROM mydb://mycat AS CAT, ls_dr8.tractor AS tractor
WHERE 't' = q3c_radial_query(tractor.ra, tractor.dec, CAT.ra, CAT.dec, 0.001)
) match
INNER JOIN sdss_dr16.x1p5__specobj__ls_dr8__tractor_primary AS tractor_sdss ON tractor_sdss.id2 = match.ls_id
INNER JOIN sdss_dr16.photoplate AS sdss_phot ON sdss_phot.objid = sdss.bestobjid
Hope this helps,
Adam