Apologies - the article you are referring to should indicate that those steps for QIE must be applied to a non-meta collection. I will create a ticket to get this amended.
In the meantime, you are completely correct in your assessment of the issue. QIE and any other change that affects how the index is constructed needs to be applied to the data source(s) in question.
If you are working with a meta collection when applying the qie.cfg you need to create this configuration file on the datasource collection(s) where the affected documents are then run an advanced update to reindex the live view (to apply the QIE to the index). It's also a good idea to create a qie.cfg on each of the other collections in the meta collection too to ensure that they get the default QIE weight applied. You would need to check that QIE is applied to documents in there by looking at the Step-QueryIndependentEvidenceCollectionLevel.log, in the live view of each of the collections.
When looking at the log file check the summary
---------------- Summary ------------
No. docs: 15235
No. with dflt score set: 15235
Command finished with exit code: 0
The 'No. with dft score set: line indicates how many of the documents didn't match a pattern in the config and received a default weighting. Any patterns you define should also appear in the summary along with the number of documents that received that QIE weight.
Note that you need to set the -cool.4 value in the query processor options (or padre_opts.cfg) within the collection or profile that you are querying (so in this case that will be the meta collection's collection.cfg, or the padre_opts.cfg of the profile you are querying). This is because the influence given to QIE weights can be adjusted at query time so the configuration for this is with the query processor options for the running query.
Because of this you can also test the effect of QIE after you've indexed by setting this as a parameter in your URL - running with
&cool.4=1 (max effect of QIE) in the URL then
&cool.4=0 (QIE is disabled). You will hopefully see a difference in the results for the two queries if the QIE has affected your index correctly.