Mongodb db.runCommand debugging

The one difference I can see between the two is that one is passing in listCollections: 1.0 and the other passes in listCollections: 1.

The value parameter for the listCollections command is irrelevant -- it exists to create a key/value pair when constructing a BSON document to pass as a parameter to runCommand but isn't used by listCollections.

All of the following are equivalent (although a numeric value makes more semantic sense):

db.runCommand({'listCollections': 1})
db.runCommand({'listCollections': 1.0})
db.runCommand({'listCollections': 'foo'})

If you are using MongoDB 4.0+, the document format can be useful to provide additional optional fields like filter and nameOnly.

Instead of passing a document as the first parameter for runCommand() in the shell, you can also just use provide the command name to run with the default options:

db.runCommand('listCollections')

Is there any way I can convert the log output above into a db.runCommand() that I can execute to see if I get different results ?

Equivalent commands in the mongo shell to your log output would be:

use datalake
db.getMongo().setReadPref('secondaryPreferred')
db.runCommand({'listCollections': 1})
db.runCommand({'listCollections': 1.0})

The listCollections queries will be processed identically. However, since you are using the secondaryPreferred read preference it is possible that this query might be returned from different members of your replica set when your two applications are running queries concurrently. Normally this will not be an issue, but if your use case requires strong consistency you should use a primary read preference instead.