Make sure the worktops cab, if needed, be made deep enough to be able to route waste pipes etc behind appliances. Quartz are popular and work very well, but pricey.
Ikea units are now a total pain to fit as they do not have a recessed back and there is only 80mm under them. I have used DIY Kitchens and found them OK for price v quality.
You may need to get the floor makeup signed off by your SE. Ground bearing is generally better if you are on level ground with no heave or shrinkage. You need this designed so you can get levels for membranes, DPCs, reduced dig, insulation, finished floor, drainage etc.
For the windows, I prefer white. Other coloured windows do not always age well and can look dated. Blue frames in public and commercial buildings from the 90s and dark brown rosewood in housing spring to mind.
For the roof a smooth clay tile will keep its colour and not attract as much moss and lichen as a sanded finish.
Can you cut a much bigger hatch and trim out the ceiling joists? A drop down hatch and a proper ladder will make regular inspection and maintenance easier.
I think the MVHR units normally have a condense trap that needs to be fed into a drain.
Was a PIV unit ruled out? They are a simple install.
Ask the SE if there is anything you are unsure of. It is what you pay them for. A normal lintel is easier to deal with. I have used the Hi Therm ones before and they give you the psi values which is useful for your SAP calcs. Maybe some of your openings are too wide, so beams are the only way?
The planning consultant could be a good call. I have, in the past, instructed architects to design a scheme that did not gain planning consent, so quite a waste of time and money.
I would favour shortlisting a couple of architects and asking each to produce a sketch scheme for an agreed fee based on your brief and input from a planning consultant.