No. Construction costs when putting roads underground is more expensive, but not extremely so when done from the start.
The additional structures that need to be built will only represent a minor percentage increase in overall building volume, so the direct additional construction cost should be affordable.
The primary cost will also not be the construction costs but those of maintenance. If changing one structure means a lot of interference with the surroundings this will make maintenance and alterations expensive. The need to maintain and alter the city as time goes by must be designed in from the start.
Buildings and roads must be built in such a fashion that they can be disassembled without blocking the transport network or damaging other structures. Pipes and cables should have separate roadways so that they can be re-routed without having to dig or tear things down. Most importantly, the buildings should be designed so that the building’s shell (basically the floors and support columns) can be last a very long time but the interiors can be removed and upgraded. Thus a block of 2 room flats can become an office block before being turned into a hotel or a shopping mall.