Yes they continue to grow roots through the stretch, after that is isn't really a problem.
you do NOT want to impede root growth during flowering because it will cause the plant to stop stretching and put all of its energy in bud growth unless you doing a SoG grow.
for normal grows its best to let roots expand through the entire process.
1 week in on a 11 week sativa
next time transplant it 1 week BEFORE flowering starts, that way the roots have a Head start. you can still do it, i transplant as far as 10 days into flowering.