First off, note that when looking at Figure 2 from the paper (shown at top) they

color in a lot of "Spinosaurus" material, which might give you confidence in the
proportions they use to reconstruct the skeleton. However, if you read the
supplemental data (and as with any paper I highly recommend you do) you will find
the Supplemental Figure S3, which has a whole lot of additional colors. In order to
interpret this you need to know that the red and rust-orange represent the newly
designated neotype and the older (now destroyed) Stromer specimens, but about all
of those other bones? Yellow is referred isolated remains (i.e. they aren't
informative in terms of proportional scaling), the green elements are based on
other spinosaurids (e.g. they are not from Spinosaurus) and the blue are "inferred"
(e.g. restored, not based on actual fossils).
I of all people won't begrudge the authors' for inferring missing bones, and they
are to be commended for the supplemental figure, which so clearly labels which
bones are based on which specimens in a visual and easy to understand diagram. But
when boiled down to the bones that impact the scaling of the specimen there is a
lot less data to work with than a reader might infer from Figure 2 up at the top of
this post. In terms of proportions, most of the newly available data only pertains
to the pelvis and the hindlimbs. I created a (rough) schematic diagram to
illustrate what we knew prior to this publication from Stromer's material (smaller
skeletal) and what we have to base the proportions on with Stromer's material plus
this new specimen (NOTE: I haven't changed the proportions or shape of the new
pelvic and hindlimb elements, this is a schematic diagram).