The wires sit on top of the transistors. Many layers of them in a modern process.

However you can't always pack the transistors as dense as you would like because you can't fit the wiring for them in above at the same density.

Plus there are various 'design rules' that constrain how things get placed. These are needed to ensure manufacturing is successful and achieved good yield. An important set of rules are the 'antenna rules' that requires the insertion of antenna diodes (using silicon reducing transistor density) to prevent circuitry being destroyed during manufacturing: https://www.zerotoasiccourse.com/terminology/antenna-report/

The wires didn't fit on the back of the envelope.

The wires run over the transistors.