I think there is a misunderstanding.
The way I read it, if you use a large number of inport and outport blocks (at the root level), the accelerator may not speed up your model very much, but there is no exclusion on using these. (This applies to the root level inport/outport blocks only.)
"Accelerator mode runs the blocks as if you were running normal mode because these blocks do not generate code for the accelerator build. Consequently, if your model contains a high percentage of these blocks, accelerator mode may not increase performance significantly."
Likewise, all "to workspace" or "to file" blocks may be used, but these are run in normal mode.