Exporting with command line: avoided shapes (Connector tool) not respected

Migrated from https://bugs.launchpad.net/inkscape/+bug/1170743

Steps to reproduce:

• save file connector.svg
• open command prompt
• run inkscape --export-file=connector.pdf connector.svg

Alternative: use inkview (inkview connector.svg) or browse the file with the "open" dialog, the preview shows an incorrectly routed file.

What happened?

The center shape should be avoided, but in the PDF, the line goes through it. connector.pdf

What should have happened?

The shape is avoided.

Issue does not occur when exporting from the GUI, although comment 3 says so.

Steps to reproduce:

1. launch Inkscape by itself
2. open the sample SVG file from within Inkscape -> routing is incorrect

Doesn't happen when the file is opened in a new (second) document window (e.g. because the empty file in the initial document window has been modified).

Inkscape Version and Operating System:

• Inkscape Version: 1.1-dev (12e2a09, 2020-02-19)
• Operating System: Windows 10
• Operating System version: 10.0.18362

Replicated since 0.48.4 r9939 (Dec 18 2012) as per Launchpad comments.