With regards to Roine Stolt's TFK, I think it's pretty clear that it is NOT an official part of the TFK discography, but more of a follow-up to the original album The Flower King, which is a SOLO album by Roine Stolt, which just happened to feature players who would become members of The Flower Kings. It's just another Roine Stolt solo album, but with a sub-title for the artist name. Seems simple enough to me, and I think it's just named that way to help sell more records, which is what a record label really wants to do, right? Sell more albums for the label and the artist to profit from and generate more revenue for everyone involved.
With regards to bonus discs/tracks, at least with Spock's Beard, they have been doing this for YEARS, well before Noise Floor came out. Feel Euphoria has 2 bonus tracks, while Octane has a whole disc of outtakes and special tracks tacked on. The self-titled 9th album, while not released by Inside Out, had a bonus disc release in Japan (though the Japanese labels almost always ask bands for exclusive material for their release so that Japanese fans can buy domestically and not import, keeping their money within the local economy). And their 10th album, X, had a special edition bonus track that was limited to early pre-orders. The eventual retail version (from Music Theories) omitted this track, but I think both versions were NOT on Inside Out. Later on, BNADS, also not initially on Inside Out, was self-released and had a whole disc of bonus tracks (a decision made by the band, I am sure).
At any rate, in the case of Spock's Beard, they had ALWAYS offered up bonus tracks for Inside Out's European releases, with demos on their first three albums, the song "Hurt" for Day For Night, and later on a bonus disc of demos/in-the-studio-jams/a cover for Snow. So at least for SB, the idea of bonus tracks for Inside Out is not a new one, and even if you consider that most of those earlier ones are just extras (demos and covers), the later albums with original songs relegated as bonus tracks, most of those decisions were probably the band's (at least in the case of BNADS, which still had one exclusive track not release by Inside Out).
It's frustrating, I know, when a disc still has room left and there's bonus material that would have obviously been able to fit on the first disc, but I think putting them on a second disc is a business decision. I remember reading that double-disc albums are counted as a sale of 2 discs when counting album sales, so an album that sold 5000 copies that was a single disc would get counted as 5000, but an album with a bonus disc that sold 5000 copies would get counted as 10000...maybe? Perhaps someone with more knowledge of the music industry can correct me, but I do recall reading this somewhere (maybe even here). If that's the case, relegating B-Sides to a seperate disc is a way to boost sales numbers for an album, which is smart in my opinion.
As for what to do with those bonus tracks? Just do what I do - come up with your own running order! Be as meticulous as you want, or just tack them all on before the closing track. Personally, I lay out my personal track lists as fantasy LPs, with chunks of 18-26 minutes of music per "LP Side", and lay out an album like that, figuring out which tracks flow well into and out of each other. It's really how I only listen to albums like Octane, BNADS, and Noise Floor (all of which have significant numbers of bonus tracks), as well as many of the Flower Kings albums (which have various bonus tracks/discs across the globe).
I don't think Inside Out is maliciously holding albums hostage before releasing them to the public, giving their artists no choice or say in the matter of which tracks should and shouldn't be on the album if they weren't happy with it. I know there have been interviews with members of various bands who probably say "I wish ___B-Side___ was on the main album", but I'm sure it was all handled in a way that was professional and made everyone happy in the end.
And to be honest, if these bands just released their music by themselves, off-label, can we really say that they would still be operating today if it wasn't for Inside Out and their help in getting some of these bands to the level of popularity they have today?
-Marc.