This method is correct for finding the scale length, but not very helpful in bridge placement. You need to have strings attached (Which requires the bridge to be attached) in order to find the 12th fret harmonic. Since you have side dots, I would suggest you measure the length from the DOT to the nut, and multiply x2. This should give you your scale length. The bridge should then be positioned so that the saddles line up at whatever scale length you determined. ie. The bridge would be 34" from the nut on a 34" scale bass.
If you do it this way, your intonation should line up correctly with the corresponding side dots.
EDIT: I'm not sure how clear that was. So i'll attempt to clarify.
The location of the 12th fret harmonic is based on the placement of the bridge. Because of this, in order to have the 12th fret harmonic BE ON the 12th fret, the bridge must first be placed in its proper position. Since you have the 12th fret position, but not the bridge position, you can measure to the nut from the 12th fret, and use that distance to place your bridge. Either use the same distance (maybe like 17", depending on what you get) and measure from the 12th fret dot. Or double it and measure from the nut.
Also, because the bass is fretless, the intonation will have to be slightly adjusted per string. I would suggest you place the bridge so that the saddle on the lowest string corresponds with the scale length you determined based on your side dots. This way the intonation for that string will be correct, you will probably have to move slightly UP the fretboard as you go UP strings to keep the proper intonation.