So what do u think? Will it work as is?
Will what work as is?
Under no circumstances can the DS1054Z keep up with 400+ Mb of USB signaling.
One of your links discusses IR capture
I'm not sure that any of the USB approaches linked above are all that robust. I wonder why they're not using TCP since it eliminates a lot of issues, particularly on Linux (permissions, device rules, driver). A telnet session is pretty easy to create for command line interfacing. Opening a socket in C or Python is also pretty easy.
So, sure, given enough programming effort, data could be captured and analyzed in code. But only for signals within the capability of a 100 MHz scope (assuming DS1054Z). Analysis is going to take some care. Samples can be anywhere in the waveform and detecting edges will take a little thought. Matching edges across mutliple channels may take a little more thought. All of the sample programs linked above deal with simply plotting the data. That takes a lot less thought.
All of these decoding projects are easier with a logic analyzer.