I have been using the Stewmac calculator for ever and have not had any issues.
The problem that guy had was not the SM calc, it was the fact he used a slipshod oops hipsh#t bridge.... They are CRAP.

Also, if you read the print at the bottom of the calc it gives you positions for the most common types and brands of bridges that SM sell and that most serious Luthiers use.

If you want to set any other bridge, do the right thing and measure your scale length from the centre of the actual 12th fret.
Had this guy done that, his slipslop bridge would be in the correct place...... But he would still have a really crappy bridge.....