Arduino UNO bootloader sketch uploading time

Hi, I uploaded an arduino UNO bootloader to an ATmega328 I have in a project I'm currently working on. Why an ATmega and not the complete Arduino? Costs, I can't afford one arduino for every project, because of the price itself and the restrictions on imports.
I've successfully made the atmega work, but only by using the arduino uno as ISP programmer, but I want to use it on something else while working, so I made the serial interface that comes on the Arduino Serial board (it's way too complicated to get an usb2serial board, even with an FTDI chip), uploaded the current arduino uno bootloader to the atmega and it works. Autoreset, serial com (with a baud rate not so high).
I'm also using arduino-cmake, and sadly for some reason I can't figure out it doesn't support autoreset with this serial interface, so I have to press the reset button in the right moment, and because it only waits for a few seconds I have to press it several times..
My doubt is, can I upload the arduino UNO bootloader to the atmega328 but with more time to wait for the sketch?

can I upload the arduino UNO bootloader to the atmega328 but with more time to wait for the sketch?

You can if you can recompile the bootloader.
It's off in the arduino install in .../hardware/arduino/bootloaders/optiboot
and you should edit optiboot.c where is says:

  // Set up watchdog to trigger after 500ms
  watchdogConfig(WATCHDOG_1S);

And change it to:

  // Set up watchdog to trigger after 500ms
  watchdogConfig(WATCHDOG_4S);

Recompile with ".\omake atmega328" (for windows, "./" for linux/mac)

Use whatever you've been using to burn the new .hex file into your chips.