No. You ignore the siege tower's shown starting upgrades, and maintain the same upgrades it had before the Builder talent was used. 

For example: A dispatch platform spire was constructed during the Build Phase, with its starting upgrades of 1 attack and 1 range. During the Onslaught Phase, the brawnen use a limited build option to add a fortification upgrade to it. Later, the brawnen use an architect's Builder talent to promote the dispatch platform into a siege tower. The architect can do so even if the brawnen don't have the Smelter Level 1 advancement. The dispatch platform chip is flipped over. This spire no longer has Splash but now has Raze, and has an upgrade capacity of 4 instead of 3. Its upgrades do not change - it maintains its upgrades of 1 attack, 1 range, and 1 fortification.