Hi evosy
Your physiotherapist did the right thing, in my experience a LLD is an over diagnosed 'condition'. A poor therapist would get you to lie on table and measure without resetting pelvic position (using the simple technique you describe), meaning if you lay down on table with 1 leg/your hips not in the exact neutral position it could be incorrectly measured as a discrepancy. The accuracy of the measurement also depends quite strongly on the therapists surface anatomy/palpation skills and last i remember the basic LLD measurements we have at our disposal are quite crude with a very poor inter/intra-tester reliability, which is to say even with this pelvic resetting maneuver its is far from a reliable measure.
Long story short, on his first look at your LLD there would have been an 'apparent' LLD but when he got you to 'reset your pelvic postion' when lying back down this apparent discrepancy dissappeared. I would not worry about it!