Can you make sure the SharePoint module is installed in VS 2017. Also try downloading the CSOM dlls from server and add reference them in your project.

Have you tried Content Query web part? It allows displaying documents from libraries based on a content type. Filters and grouping is also available.

@Klj126 can you increase the list view threshold value in central admin just to make sure if this is causing the folders invisible

Can you try creating a site collection with Team Site template on the UI and then activate the SharePoint Server Publishing Infrastructure site collection feature?

Can you create a new workflow on a new list to isolate this issue if it is across whole SharePoint or just with that list?

Have you tried running a full crawl? Moreover, have you included RefinableString00 in the search display template?

Can you create a new list, add a folder and an item? Go to Content and Structure and see if the folder is visible? This would isolate if the issue is across whole SharePoint or just with the specific list.

Can you make sure the user that runs the powershell command to create a publishing site is same as the one who creates it on the UI?

Also make sure the Workflow Tasks list has Approvers group added.

Have you tried Microsoft.SharePoint.Client.File.SaveBinaryDirect with clientContext.PendingRequest.RequestExecutor.WebRequest.Unsa‌​feAuthenticatedConne‌​ctionSharing = true;? By the way, CSOM uses WCF services to talk to SharePoint so in your case server object model is a good choice. Moreover WCF runs over http which is an extra layer. Server object model apis talk directly to SQL Server SharePoint using binary code.

Please open the page in Google chrome and go to console and paste this ctx.overrideFilterQstring; to make sure the required information (in your case its heading) are there. Can you post that in your answer?

Can you confirm the headings that you like to have nicely formatted on the page exist in the url? If yes, could you also post the sample urls in your question?