Okay, sorry for another double post, but I have fixed the Wayfinder code is a very simple, but effective way that I believe is the way it should be in the first place.
Let me give a brief explanation before I post the code. In the PHP code, Wayfinder cycles through every document that will be represented on the menu, and for each one, it uses a series of if...elseif...elseif... etc statements to check to see if a certain type of template (such has hereTpl) should apply to the document’s menu item.
Here is the original elseif statement for the activeParentRowTpl template check:
} elseif ($resource['isfolder'] && $this->_templates['activeParentRowTpl'] && ($resource['level'] < $this->_config['level'] || $this->_config['level'] == 0) && $this->isHere($resource['id'])) {
This checks to see if the document in question is a folder, checks if activeParentRowTpl is even specified, checks if the document in question is at lower level (higher in hierarchy) than the level specified in the Wayfinder call (if if the level was set to infinite recursion), and checks if the document in question is in the parent tree of the current document.
In a normal, single menu with top level documents and their children, activeParentRowTpl will be applied correctly because the current child document would be in the menu, and each parent document would be at a lower level number (higher in hierarchy) than the level specified in the Wayfinder call. However, in my situation where the child documents’ menu items are in a separate menu, the activeParentRowTpl is not applied to documents’ menu items who are parents of the current child because the child is not on the same menu, and therefore the level specified in the Wayfinder call doesn’t go all the way down to the child, so the check for a lower level than the specified parameter fails and the template is not applied.
To make this work properly in all situations, rather than check if a document in question has a lower level than the level parameter, the level needs to be checked against the level of the current child (which is in the other menu in my case). Because the child isn’t included in my main menu, I couldn’t just get the level of the current child. However, what I was able to figure out is that Wayfinder uses a isHere() function the checks if a document in question is the current document or any of its parents, grandparents, etc. Since the elseif statement for the activeParentRowTpl template already checks to make sure the document in question is one of those documents, all I needed to do was remove the code that checked the level of the document and replace it with code to ensure the document in question is not the current document. The result is that the activeParentRowTpl template will always be applied to the parents, grandparents, etc of any current document, no matter if the current document is in the same menu. Here is my updated elseif statement:
} elseif ($resource['isfolder'] && $this->_templates['activeParentRowTpl'] && $resource['id'] != $modx->documentObject['id'] && $this->isHere($resource['id'])) {
In case I just made that all way more confusing than it needs to be, here’s what I did in simple terms. When considering applying the activeParentRowTpl template to a document in the menu, I told Wayfinder to determine is the document is a parent, grandparent, etc of the current document
even if the current document does not show up in the same menu. With the original code, the activeParentRowTpl template would only be applied to parent documents of the current document if the current document was in the same menu.
I hope somebody else can benefit from this, and I’ll see about contacting the author to see if he/she is interested in updating the Wayfinder snippet to use the code I have discussed here.
Thanks for the suggestions and help, everybody.

I’m considering this problem solved.