Hi there, I assume by bleed nipples you mean the small pin that sits in the centre plate of the thermostat. Normally referred to as jiggle pins .I have never seen a thermostat with out a pin in it.
Yes it is important to get it in the right way and not upside down. Is it possible you have got it the wrong way round and that is why you are having trouble sealing it. It could be bottoming out in the housing.
Would have thought your mechanic would know what way round to fit it though.
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