The pull-up and cap are required for reliable everyday operation, so they must be on the final PCB. The boot and reset buttons may be on the PCB, or on the programmer.
Bodging the cap and pull-up resistor onto the board will be just fine for determining whether that is all that is missing. Since EN isn’t some fast signal, it isn’t important that they be super close to the -S3 chip. Bodging them onto the programming connector, for example, should be fine.
Something to consider for your next version: JTAG for debugging. On the -S3, those are pins IO39-IO42. With that, you can do step-by-step debugging using the official ESP32 programmer, ESP-PROG, which is very inexpensive, around $11. (They just released a new version, ESP-PROG-2, but I haven’t tested it yet so I can’t say whether it works with PlatformIO, in case you’re not using ESP-IDF.)
The ESP-PROG boards use an FTDI chip to do both JTAG debugging and serial programming, and include boot and reset buttons. On my own ESP32 boards, I now use the miniature 1.27mm-pitch connectors of the ESP-PROG boards, so I can program them with that.