Hi Jacopo Del Vivo, welcome to the OS2World forum.
For what I know, I never know about a procedure to install eCS (eComStation) from an USB Flash drive. On those days, it was always needed a DVD drive to install the OS. There were some other technique to clone the HDD image from an installed machine to other one.
Today, I use
ArcaOS 5.0.6 and I install it from a USB flash drive, since that OEM version of OS/2 has formal support for it.
I never installed eCS from an USB flash drive, I don't have much experience with Rufus. I don't even remember correctly if the latest version of eCS, 2.2 beta II, (December 2013) was able to boot from an USB DVD drive. Also, we haven't get any news about eComStation and its company since 2014.
If someone else has some experience, please let us know.
Regards