I don't think that there is any official/legal definition of "second fix". There may be something in caselaw precedent, but nothing comes to mind.
Normally in cases like this, it would fall back to the concept of "custom and practice". In which case all non structural internal timber work is "second fix". Generally, if its planed, smooth timber, and something that would normally be painted or stained, then it's second fix.
It's certainly not decoration - which implies something that would be regularly changed or updated
What you could say to your builder is that you will jointly go to one or more independent professionals for an opinion (say, an RICS member) and be bound by the consensus. And with the understanding that the person who was wrong pay all the fees.
However, I would have concerns about your contract clause. "In essence, all works required to second fix to make the new build habitable" says to me that the property only has to be habitable ... ie you can occupy the property perfectly well without skirting and architraves. Some properties do not even have any
Further, "to second fix" is very vague .... is that up to second fix (ie before) or after?
There is potential for different interpretation of that clause, but its badly worded. I'd not like to rely on that clause
I would go down the route of referring this to a professional for an opinion, and infer that while you are at it you might just get that person to inspect the whole work to see if it is up to all relevant standards
Either way, do not pay for the work until this is sorted out. In contract terms, you have a dispute and you are entitled to withhold "reasonable payment" and involve someone to mediate or decide the disputed items. Don't be intimidated by anything the builder says, and bear in mind that he must still adhere to his other contractual obligations