Hi Matt,
Thank you for taking the time to examine my test model. The smallest pipe diameter downstream is 2" (not 8") as this is how I left the model right before attaching. If I keep the 2" pipe in place, convert #76 to a junction, and run the model without any other changes I get the following results:

This doesn't make sense to me as it is showing no ponding, even though the WSEL is clearly backed up above the rim elevation of the junction. How did you get the results to show a flooded volume for this junction?
I do see the comparison you are trying to complete. If the downstream pipes are backing up the WSEL above the rim of the sag inlet it should cause ponding. This ponding should not disappear if you change the inlet capacity of the inlet. I can test this by causing a backwater condition in the downstream system (with a 2" pipe) and then running different types of grates/sweeper inlets.
In scenario #1 I purposely restrict the sag inlet with a very small grate and get the following results:

The calculated gutter spread and gutter flow depth appear to be based on the inlet capacity only and are incorrect as ponding should be occurring due to the backwater condition. If I look at the excel inlet report however I do see that ponding is occurring:

In scenario #2 I greatly increase the inlet capacity with a sweeper inlet and get the following results:

Again, the calculated gutter spread and gutter flow depth appear to be based on the inlet capacity only and are incorrect as ponding should be occurring due to the backwater condition. Also again if I look at the excel inlet report ponding is occurring, and its the exact same volume and time as the much smaller inlet:

This appears to show that SSA is correctly determining when ponding is occurring but is displaying it in the results incorrectly. A gutter spread and depth of flow should NOT be shown if ponding is occurring unless they are correctly calculated based on the ponding volume and cross section of the pond which SSA does not appear to be doing.
Regarding a gutter cross section vs pipe cross section for bypass links, I have been trying to determine how much this effects the model and also have referenced some other modelers to see what they do. FDOT uses a direct link, which is odd as I have been unable to get this to work in any SSA model. This modeler recommends using a pipe with a length of 1' for all bypass links. I have tested this myself by making a copy of a model where one version is 1' long bypass pipe links and the other is exactly the same except all the bypass links are a gutter cross section. I overlaid the results in SSA and was unable to see any real difference:
Would you have time to run a similar modeling comparison and see if you can find differences in the results when bypass links are modeled as pipes versus gutters?