In the nicest possible way, you really need to discuss this with your doctor and until then follow exactly the instructions on the packet.
The advice for "ordinary" formulas is based on the fact that there is a tiny chance that the powder may be contaminated with a potentially harmful bacteria. Using water above 70 degrees kills this bacteria and has no negative effect on the nutritional value of ordinary formula. So to address this tiny but serious risk, the advice is to use the hot water for ordinary formula.
For some babies, presumably yours included, a speciality formula is required. Some of these formula contain special versions of nutrients that would be damaged or destroyed by the hot water. So now it becomes a question of balancing risks. The risk of the bacterial contamination above versus the risk of the baby not receiving adequate nutrition because the hot water has destroyed certain ingredients. In this case, the medical evidence is that the risk of malnutrition outweighs the risk of bacteria and so the advice is to use water (previously boiled) at room temperature. Unfortunately in this situation, you can't eliminate all risks but please know that the bacteria risk is very infrequent indeed - and some other countries like the USA advise the room temperature method for all formula.
Of course you want to do your best for you baby. You can minimise risk by practicing scrupulous hygiene when making up bottles (thorough hand-washing, immaculate surfaces, etc) which I'm sure you do anyway.
I hope this helps you understand why the general advice doesn't apply to the specific cases of speciality formulas. Honestly using room temperature water is a lot less hassle than the other method so you could see this as a silver lining in whatever issue has caused your baby to be prescribed special formula. Best wishes to you.
And please talk to your doctor with any questions.