Change in rotated NMDS scores as a response variable

Hello all,
I'm interested in adapting a technique from a recent paper

Harrison, S., E. I. Damschen and J. B. Grace 2010. Ecological
contingency in the effects of climate change on forest herbs.
Proceedings of the National Academy of Sciences (USA), 107:
19362-19367.

In which a plot's change in NMDS scores over time was used as a
response variable:

"To measure the overall resemblance of any given herb community to
communities found in warm (steep, southerly) versus cool (moderate,
northerly) topographic microclimates, we used an ordination approach
(also see 28). We ordinated the
herb data using NMS ordination in PC-ORD version 4.14 (39), excluding
species found in <5% of samples. We rotated axis 1 of the ordination
to maximize its correlation with Whittaker?s topographic moisture
gradient, so that a low axis 1 score indicated a community in a mesic
environment such as a moderate north-facing slope, and a high axis 1
score indicated a community in a warm environment such as a steep
south-facing slope. Under a warming climate, we expect the community
at any given site to show a higher axis 1 score in 2007?2009 than in
1949?1951, indicating that herb composition has shifted over time in
the same direction that composition changes over space from mesic
(cooler and moister) to xeric (warmer and drier) topographic
microclimates. For each site we calculated the difference between its
1949?1951 and 2007?2009 axis 1 ordination scores. In this case, a high
value means a community that has shifted to become more dominated by
xeric-adapted species."

Jari Oksanen has a post on the the r-forge page
(https://r-forge.r-project.org/forum/message.php?msg_id=1311&group_id=68)
warning against using rotated NMDS scores in a Structural Equation
Model. Are there problems with using a "change in scores" as a
response variable in this kind of hypothesis testing?

This was done in PC Ord.  Has anyone used "metaMDSrotate" in vegan to
do this kind of analysis in R? Does anyone have any examples or code
they'd be willing to share or point me to?

Thanks,
Erik