How to connect a W25Q64 3.3 SPI Flash to a 5V Arduino Mega?
Assuming you don't plan to use the chip in anything but standard SPI (not Dual- or QSPI), then all the signal pins are unidirectional!

That means that in the Arduino->Flash direction, a voltage divider that divides 5V down to 3.3V is sufficient (place it close to the receiving end, usually). This applies to the clock and the master-out, slave in (MOSI) data pin (called "Data Input" in the flash datasheet).

In the opposite direction (MISO / Data Output), there's little you can do to ensure reliable transmission but buffer. A buffer doesn't have to be large – in fact, a dual-NPN package would totally do with two resistors, and that would take single-digit square millimeters in SMD. 

You might simply want to invest 33ct into something like a 74LVC1T45. That thing is maybe 1.7×1mm² in size even in its largest variant; I doubt that will be a limiting factor for your circuitry.