It should work without problem. The bug related to the "missing" SSIF files has been introduced relatively recently (with a change in the way the free disc space is checked), but before BD3D2MK3D did not require the SSIF files, and should still not require them.
The only difference with a "real ISO" (with the SSIF) is that BD3D2MK3D skips now the test for sufficient disc space. You must therefore ensure yourself that you have enough free space before launching the creation of the project and before launching the encoding itself. The rest should be OK.
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