The numbers from that article were from mid-season and were not complete by any means.
Here are some more complete numbers (nbawowy.com) of the various front court pairings and trios that Toronto used this last year:
(Regular season only, AJ = Amir Johnson, JV = Jonas Valanciunas, TH = Tyler Hansbrough, PP = Patrick Patterson, JJ = James Johnson(SF))
AJ + JV : 1254 minutes, 2399 possessions, ORtg 106.0, DRtg 107.9, Net -1.9
AJ - JV : 725 minutes, 1430 possessions, ORtg 114.1, DRtg 106.0, Net +8.1
The following are w/o Valanciunas:
AJ + PP : 494 minutes, 969 possessions, ORtg 113.9, DRtg 107.0, Net +6.9
AJ + TH : 130 minutes, 249 possessions, ORtg 117.5, DRtg 101.8, Net +15.7
The following is w/o Valanciunas, Patterson or Hansbrough:
AJ + JJ : 75 minutes, 159 possessions, ORtg 106.3, DRtg 101.9, Net +4.4
The following is w/o Valanciunas or Hansbrough:
AJ + JJ + PP : 118 minutes, 221 possessions, ORtg 109.1, DRtg 109.1, Net +0.0
The following is w/o Valanciunas or Patterson:
AJ + JJ + TH : 35 minutes, 65 possessions, ORtg 123.1, DRtg 76.9, Net +57.2
The following is w/o Valanciunas, Hansbrough or Amir:
JJ + PP: 161 minutes, 312 possessions, ORtg 112.5, DRtg 119.9, Net -7.4
The following is w/o Valanciunas, Patterson or Amir or Stiemsma(since he actually played enough with JJ & TH to pollute this sample unless I exclude him):
JJ + TH: 39 minutes, 78 possessions, ORtg 107.7, DRtg 91.0, Net +16.7
The following are w/o Valanciunas, Amir (or Stiemsma):
JJ + TH + PP: 321 minutes, 591 possessions, ORtg 120.5, DRtg 102.7, Net +17.8
TH + PP : 729 minutes, 1368 possessions, ORtg 119.6, DRtg 107.8, Net +11.8
Ignoring the more extreme numbers from the two under-40 minute samples, the main takeaway I would get from this is that Amir's lineups without Valanciunas were all positive, with exception of the AJ+JJ+PP one, which is even. If you trim that one to lineups that exclude DeRozan, though (92 minutes) it becomes a Net +1.8.
In fact, Amir's lineups in general, with both Valanciunas and DeRozan off the court, were all solid:
AJ w/o (JV, DD) : 325 minutes, 638 possessions, ORtg 115.4, DRtg 103.7, Net +11.7
Toronto's perimeter was not a very good defensive perimeter. DeRozan was not the only problem. But he compounded it with his inefficient (yet high usage) offense.
EDIT: Added the "TH + PP" (no JV, AJ or GS) front court combo.