Black-Ash Inheritance EP was separately recorded and released shortly previous to Whoracle though so it makes sense being on EP as opposed to being on Whoracle. TMT EP was probably due to the Japan bonus stuff that they have to do. It's a weird phenomenon though with many bands, I always feel like bonus tracks are always really strong tracks, and not just weird tracks that doesn't fit on the album. Same as with on Siren Charms, 2 really strong songs as bonus tracks, if I remember correctly they said they were much weirder songs they didnt feel fit the album or something.
Most of the bonus/EP tracks for IF are understandable to me. As you say Goliaths (and acoustic medley) were recorded before Whoracle, so understandable that they're on an EP (even though Gyroscope is also on it, and that made the album). Man Made God is a cool track but doesn't really fit on Colony imo so I understand why they'd choose to have it as a bonus. Clad in Shadows '99 is a remake of an older song so, again, makes sense to be a bonus - although Behind Space '99 is on the actual album, so... yeah.
World of Promises and Strong and Smart are covers so, again, makes perfect sense for them to be Clayman bonus tracks. Watch Them Feed is a really weird song that doesn't feel like it fits on an IF album so I can see why that's on an EP. Land of Confusion is a cover so, again, makes sense that it isn't on an album.
I think Discover Me Like Emptiness is the only bonus off STYE? I think it's a really nice song, although I can see why they left it off the album. Should have replaced Bottled with DMLE though. Don't think CC had any bonus tracks?
Then we get to ASOP. The Mirror's Truth EP literally contains three songs in Abnegation, Eraser and Tilt which are better than pretty much anything on the actual album - especially Eraser. Granted they don't fit the theme of shit lyrics and bad vocals, but for fuck's sake. They made Abnegation worse from the early demo version, though, so maybe best that didn't become an album track. Eraser and Tilt should 100% have been on the album though. A weird experimental track like TCP should have been on the EP, but then Anders wouldn't have been able to show off his crooning broodiness in all its "glory".
SOAPF was another that had no bonus tracks to my knowledge, other than instrumentals and remixes.
Become the Sky and The Chase are easily two of the best tracks on SC for me. The only reason they don't fit on SC is because they have energy which doesn't come from trying too hard to be "heavy" - and apparently that's not what they were going for.
A similar story with Battles. Greatest Greed and Us Against the World are decent tracks. Significantly better than the likes of Underneath My 4Skin, Here Until Forever or Save Me. They'd fit fine on the album too, so, it's more like Battles Extended than bonus tracks.
For me the bonus/EP tracks made sense up until ASOP, as they were pretty much always covers, remakes or odd songs that didn't necessarily fit on an album but were good enough to be released. Since the TMT EP though IF seem to have gone down the route of making the best songs bonus tracks. SOAPF is the only recent exception, and that's just because every song (except All For Me) was so awesome that it had to be on the main album.