Yes, you are "supposed to" finger a little bit behind the dots (and/or lines) on a fretless bass.
The dots on the side of a fretless electric bass neck are not placed for good fretless intonation. They are simply placed where frets would go...on a fretted bass. They don't work for good intonation on fretless...unless your fingertips are shaped like triangles. But they aren't. They're imperfect ovals, with a flat side, therefore the string does not ring all the way to the middle of your finger, but from the edge of your finger. Bottom line: You finger right on the dots, you are sharp.
The point where the string starts ringing, i.e. the edge of your finger, is what is supposed to be on position – not the center of your finger.
Using a tuner to find proper position is pointless, aside from calibrating your octave position. It will become second nature to squeeze, ease up on, and perhaps roll, slide, or shimmy your fingers a bit during a song, to tune your notes to be harmonious within the composition that you are playing at any given moment.
The goal isn't to be perfectly in tune, but to be harmonious with the other instruments – because perfect tune in the technical sense rarely sounds "correct" to the ear. If you play fretless, this tuning happens near instantaneously (as long as you can hear yourself well enough for your unconscious brain to take over for you).