I hate to break the mood here, but almost all metal bands piece their music together. Almost every band uses Pro Tools and record riff-by-riff, until they have their arrangements set out. There is nothing unique about Opeth in the respect that they riff-patch. Speaking of which, it was only noticeable to a great degree on the first two albums. After MAYH their songs boasted more standardized structures, so I don't see where the complaint is coming from in the first place.
Songs as a whole? How exactly do you write a song as a whole? I know the human mind is only capable of working on one thing at a time. Ever after the first two albums, there HAS been more focus on the songs as a whole, especially going with the concept albums, which quite obviously neccessitate that the songs be conceputalized along with composed as a whole. The fact that their music may at times be unpredictable, does not in any way suggest that there was no vision of the song as a whole.
Actually going with song structure tightness, you see what happens when Opeth try to go overly standard. You get Deliverance. You get an album that makes sense structurally, yet can bore the living shit out of someone because it's so repetitive and bland. The more standardized Opeth get, the worse their music will get... it's as simple as that. All a band has going for them is their uniqueness, and the more they conform to what people want, the more stagnant they will get and thus the people who criticised Opeth for their riff-piecing will in turn criticise them for being boring. It's a vicious circle, but it needs to be said that a majority of fans are fucking morons and don't know what they want from music.