All depends on location and general market. Around here doing point or Sq' is a bad idea, 90% of the work is custom homes, and by custom I mean UBER-CUSTOM. T&M @ $90-120 hr, or bid generated by gross estimate of same cost basis after pouring through every single detail and elevation. You need to charge for what you want to make, and perform, or loose it in back charges....
For instance, every outlet in the whole house I'm roughing now (Formerly owned by our Mayor) must be leveled to 1/8" tolorance 1/2" above baseboards, that will be leveled on the whole floor from a single point, with specific locations dialed out on the elevations. Zero tolorance on lighting! If an outlet or any of the 200+ recessed cans hits framing, they re-frame for it..... Layout alone is 3/4's of the actual work.
Even on speculative no-brainer D&B's the bids go out the same way, with fudge factors depending on the GC, Hassle and Tripe factors too for full adjustment of final price. Depending on the street, add parking in too.
Really its the only way to stay alive here, but I am in a rare market - The Soveriegn Island of San Fransico. (One of the most expensive markets in the country.) Drive across a bridge, different ball-game completely. Price by point and Sq'.....
"Well - I oughta....." -Jackie Gleason