What they did was the only option for you to keep the tracker portion.
It was the norm to give site mortgage and then when ready to build a new mortgage for the total would be applied for and part of it used to pay off site mortgage, new mortgage would always be at the prevailing rate at time of issue. Now had trackers still been available that is what would have happened.
In your case the original site mortgage was a tracker but by the time you were ready to do the build mortgage trackers were no longer available (I'm presuming as not 100% on the dates they finished in each bank) therefore the bank couldn't issue the new mortgage for build and site amalgamated at the tracker rate. They had to do a new mortgage for the build and if they did one for the total to clear the site mortgage as well you would have lost the tracker rate you already had so what they did was your best option.
You were never going to be able to just increase the existing site mortgage at the same rate it was on regardless of what type of mortgage/rate it was. Forget about trackers for the moment and let's pretend the site mortgage was a 5 yr fixed at 2% and by year 2 of it you were ready to build and wanted an extra 100k but rates were now up at 5%, in that situation you would also be unable to increase your 2% loan to cover the new borrowing and the alternatives would be the same, do a new loan at 5% to cover the lot or leave the 2% one alone and take new loan at 5% for just the additional amount.
Yes it causes a problem for switching but the same problem as if you had any tracker, do you lose it to go to another rate, have to do the sums to see whether it's worth it or not.
Having two mortgages on the one property is not that uncommon and doesn't cost any more generally than having one, in your case if you had only one it would be at the rate applicable when you started building as at that stage to get one mortgage only you would have had to do the new mortgage at that day's rates and clear the existing site one so your case it has allowed you to keep some bit of a tracker rate all this time.