Dave-- I have the Bowman sets and collect variations, but on those sets I limited myself to variations listed in SCD or the Registry. I needed limits somewhere because on my Topps sets after doing the SCD/Registry variations I started doing any and all recurring print defects or variant cards I could find, including for example the many different recurring color backgrounds in the 1952 set.
Your post brings up to me the question of what is a master set. I do not think there is one settled hobby definition for any particular set or in general. For some it is the variations listed in SCD, or Beckets or the Registry, or all 3. There are some avid variation collectors on this board, as evidenced by the never ending variations thread. I also post on a board dedicated to variation collecting specifically.
I think it was Huggins that sold what it referred to as a Topps Super set a few years back. It had all the variations listed in SCD, Beckett or the Registry, plus several more ( what I would say are recurring print defects or variances). It did include back stock differences ( gray/white), and I think die hards do include those, even though on some sets, such as the 1952 Topps set, completing the set that way is a daunting task. There have been threads here about what constitutes a master 1952 set and my guess is that there is still not a full consensus answer, and the answer is subject to change through discovery anyway.
On the 49 Bowman set I too would defer to Ted's expertise. But I think the
definition of a full master set, or for that matter what constitutes a variation that should have full hobby recognition, are unsettled hobby mysteries ( at least to me

)
Sounds though like you have some Super 49 Bowman sets