The test in its current form contains two mutually-contradictory assertions:

<assert>not(map:contains($result, "output"))</assert>
<assert>$result("output") instance of xs:string</assert>

In addition, the assertion 

contains(map:keys($result), 'fn-transform-45.xml')

is highly dubious because contains() expects a single string and map:keys() delivers a sequence of atomic values.

The result map actually contains a single entry whose key is something like

"file:/Users/xxxx/yyyy/QT3-test-suite/fn/transform/sandbox/fn-transform-45.xml"

which will vary from machine to machine. The previous version of the test used $result?* to access the entry regardless of its key, but this was changed to avoid use of XPath 3.1 syntax. I think we can achieve the same effect, given that it is a singleton map, using $result(map:keys($result)[1])