Progskeet is solely design for all NAND memory chips (no matter what device that is, iPhone, Wii, X360 ... you can use this modchip to it).
While E3 Flasher is only designed for PS3 SLIM no more no less, there might be a support for Phat consoles but it's still a PS3 console.
In terms of support, E3 might give you a better support for PS3 using their specialized software to do the job while Progskeet, you might need to use some officiall dev tutorials to downgrade your PS3.
Model: CECHC04 PAL/EUR 60GB SKU Console
Firmware: REBUG 3.55 CFW [DEBUG MODE, DEBUG XMB, MENU OPTION 2]
BM: Iris Manager v1.2 (Hermes Syscall8)