Yes, I would say the only true advantage is the slightly better compression. In the days of 4TB hard drives I would say this really is a non issue. Take a single CD, call it 800MB. Based on that sample set:

FLAC -> 469.7MB
APE -> 444MB

25MB difference per CD is nothing...

APE has less support compared to FLAC so it's a no brainer to me. I haven't done this myself after ripping all my old stuff to MP3 a long time ago. I now rip to FLAC always.

The only FLAC con is listed as "no bybrid/lossy" mode. USing that would kind of defeat the purpose of using FLAC so that's a non issue.

I didn't see a "gapless" feature. I know FLAC is but I presume APE is also since it's reconstructing the original sample data 100% intact.