What boiler is it, and what exactly do you mean by hole not filled in?
Vaillant and Intergas (definitely), and W-B (I'm pretty sure) explicitly state that it's acceptable to core a 125mm hole for a 100mm flue, and use the rubber ring provided to make the external seal, without the requirement to bond to the building fabric with mortar.
150mm hole needed and a flat wall surface for the worcester bosch greenstars and they still require you to seal the hole with expanding foam or sand and cement from the inside.
never seen it advised on a vaillant or intergas but i aint fitted either for a few years tbh.