Not all HETAS installers are the same! And TBH I’ve seen too many supposed competent builders not show one ounce of best building practice / common sense whilst trying to install something as straightforward as twin wall flue!
Get the flue installed during the build, or at least the section from above the stove through ceiling and roof, leaving enough pipe exposed with some plastic sheet covering the hole and secured by means of the flue joining clips so the flashing and tiles can be done, it’s much less disruption and mess and the flue can be properly routed and fixed through any joists and rafters with the appropriate clearances, the exterior flashing can be fitted whilst the roof is being finished, which means roof battens can be adjusted easily and thereby, properly. If it’s a pitched roof obviously. When it’s time to install the stove, the rest of the external flue can be fitted and bracketed 🙂
My last piece of advice would be to avoid the cheap stainless steel flue systems. They do not perform well and can cause lots of burn issues. Check out SpecFlue for the better quality systems. 🙂