'Scale elements': linked flowed text offset instead of scaled

[su_v]

Linked flowed text in legacy files may get incorrectly offset (and not scaled) when the option to 'Scale elements' to 96dpi is chosen on open in Inkscape >= 0.92.

Steps to reproduce:
1) launch inkscape with default prefs
2) open attached SVG file
3) choose 'Scale elements' when prompted

Expected result:
The position of the linked flowed text matches the static copies (green fill) and clones (green stroke) of the flowRegion elements.

Actual result:
The linked flowed text object is offset (higher up on the page) and not scaled compared to the unlinked clones (paths with green fill) of the paths in the original flowRegion elements.

Notes:
'Scale elements' of some documents with linked flowed text objects is affected by the preference setting:
'Behavior > Transforms > Store transformation'

The issue reproduces as reported with the default setting:
[x] Optimized

The reported issue does not reproduce after switching the setting to:
[x] Preserved

The attached test case is based on the original file 'share/examples/flowsample.svg'. The current version in the repository (lp:inkscape/0.92.x) was scaled as described and is affected by the reported issue (linked flowed text offset, text layout changed compared to original version).

TODO:
Figure out a reduced test case, since the described behavior so far has not reproduced with new files created in 0.48.x or 0.91 from scratch.

Reproduced with Inkscape 0.92.0 r15299 and lp:inkscape/0.92.x r15309 on OS X 10.7.5

[jazzynico (jazzynico)]

Also reproduced on Windows XP (32-bit), lp:inkscape/0.92.x rev. 15309.

[su_v (suv-lp)]

Crashes (preview image in file chooser, or on load) with Inkscape 0.92+devel r15407 (default prefs) on Ubuntu 14.04.