If anyone is interested, I put this project together and I just received the PCB and with this setup, you can program and work with the ESP-01 boards just like you can with any Arduino... no need to manually reset before the upload etc. The circuit handles everything for you so you can just upload and then drop into the serial monitor and it all works quite nicely.
that doesn't have the automatic switch between programming and serial communication you have done in you project.
Maybe you forgot wich board to choose in the IDE, maybe nodemcu or wemos mini?
Serial communication with the ESP-01 module works just fine after it is programmed... as I said, with this board, it works just as if you had a USB cable connected to an UNO and you uploaded a sketch ... the behavior is identical.