If a patient has a gfr in low 40's but only trace protein in urine are they still considered to have stage 3 ckd?

Yes. : Proteinuria increases the risk and the progress, but staging doesn't change for me.

There are some new: Criteria using values other than GFR to diagnose type and severity of kidney damage. But yes, GFR of <50 is criteria of stage iii kidney injury/failure, regardless of presence or absence of proteinuria. The important thing at this stage: aggressively treat and decrease effect of causative factors, as often, the gfr/ kidney failure can be improved. Please talk with your nephrologist (kidney doc).