DSP Builder Advanced vs Mixed mode (Basic + Advanced)

You can't mix the blocksets as such: the Advanced blockset design can only be a single (hierarchical) subsystem within a standard blockset wrapper.

The pin assignments may be doable in other ways, although more manually, such as a *_assignments.tcl file which gets included when Quartus is run interactively (via the Run Quartus block which calls run_quartus_block_open.m).

Alternatively DSPBA_Features.additionalQuartusTclSettings is a string that is inserted into the .tcl file after all the other set_global_assignment calls.

There isn't a download to target flow yet.

Not sure about any advantages of Subsystem builder.

I think of it as Standard block-set being more WYSIWYG and Advanced being more HLS - i depends on the style that suits you; but I'd use Advanced block-set wherever possible.