'We added more skylights upstairs post-build. Possibly the framing could be specified from the outset to allow for apertures in the potential locations for skylights when it is not certain that they are going to be required. '
This is a good one to consider. Often when you are building a house or alterations it's not until the framing is up or the project even completed that you discover what you could have done to improve it. Or you may want to do something but the budget doesn't allow it at this stage.
Skylights are a good example of this. The fun fact is unless you are having one made to suit, the proprietary types don't come in sizes that fit nicely into standard rafter widths.
So, how do you accommodate this? The best way is to try to anticipate these sorts of later additions in your early design phase and allow for them in the documentation. The framing can be built and lined in for later installation with less disruption to the structure and wont trigger further consent applications. You are better to get as much as you can consented in the main consent and then choose to take it out later than trying to add things in during or after the build as you'll end up paying more in consent fees, and could cause delays in construction.
Take advantage of the tools that architects have available to them. 3D walkthroughs and models are integral to architecture software so ask your architect to provide you with these in the concept phase. If they aren't using 3D capable software you probably should consider going elsewhere!
Another option is spacing your rafters further apart (assuming it's a raking ceiling), this may require upsizing all the rafters however to accommodate the longer spans, so could be an added cost that may be better utilised elsewhere if it's only a 'could do later' kind of thing.
As hindsight manages to win over foresight more often, during the framing stage is the next best time to deal with these. Spend the time on site before the wall and roof claddings go on as you have a much better idea of the spaces and how they relate to the sun or views. Be mindful however that large scale changes like these can mean an amendment is required with the council and that can hold up works on site. And these changes can also test a builders patience!