yes, you have now described the situation perfectly.
turns out there is no need to keep toggling boot0. no need at all to ground during development. for stand alone there is no need to ever bring it high. you will notice in the eevblog thread it started out with a switch attached then described as hardwired later on.
Ok, so what you are saying is that in "development" mode, i.e. with USB-serial programmer attached, BOOT0 is always set high. Any reset will enter the ROM bootloader, and DTR is connected to RESET pin.
When you have finished development, (the USB-serial can be detached or just used for regular comms), BOOT0 is set low. Then any reset will start user code.
So it seems like a jumper or switch on BOOT0 is required in that case. A fully automatic method would need an extra line such as RTS.
I have a cheap FTDI breakout
FT232RL which is similar to Sparkfun/Adafruit ones at 10x price. It has DTR/RTS available on side connections, but only DTR on the end connector. (See pic)
The other cheap chips (CH340, PL2303) don't seem to have full modem signals available. The FT232RL is <£3 and available from local distributors.
There are some cheaper FTDI chips (e.g. FT230X) which have 4 configurable IO lines, which could be used for custom purposes, but it would mean using the special FTDI drivers instead of the stock UART/COM port API.