How to interpret the SMRT Link base modification algorithm output?
It sounds like you're looking for the modifications.csv file, rather than the modifications.gff file. The .gff file is for viewing in SMRT View (or other viewers). You can see schema for both files at PacBio's Methylome Analysis Technical Note. Specifically, modified_base means the algorithm could not determine the exact base and modification.

I also found a video tutorial for performing the analysis in SMRTLink on YouTube

EDIT: Per PacBio's Methylome Analysis Technical Note documentation, the .csv "...is also produced when motif analysis is not active, such as with the RS_Modification_Detection analysis protocol." Not sure why it's missing, perhaps because the algorithm couldn't clearly identify any of the modifications. You'll probably need to contact tech support on this issue.

In either case, the .gff you posted includes the significant hits (p &lt; 0.01), but the algorithm was unable to classify them, likely because of insufficient coverage. PacBio's Methylome Analysis Technical Note documentation gives specific coverage recommendations for each event type, but 100x is the lower bound. Lots of good information there. 

Probably not what you wanted to hear, but I hope that gets you going.