It sounds like your real question is how to install PDFtk on Azure WebApp for Windows.
Yes, I tried to install it and run a command pdftk.exe *.pdf cat output combined.pdf successfully.
Here is my steps below.
I downloaded an installation PDFtk Free from PDFtk offical website https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/.

I installed it into D:\Program Files\PDFtk my local Windows machine and move into the directory PDFtk\bin.

I was ready for two PDF files, such as Google.pdf and Bing.pdf which I got them via browse and print them as pdf in Chrome.

I opened the Kudu console of my Azure WebApp, and command cd site\wwwroot to move to wwwroot path , and then I drag and drop these four files above in Step 2 & 3 into it.

Finally, I tried to only run pdftk.exe to get the help information successfully, and then to run pdftk.exe *.pdf cat output combined.pdf command and it works fine to get the combined.pdf file as Step 4 shown.

So if you want to invoke it in programming, you just invoke its absolute path D:\home\site\wwwroot\pdftk.exe with its parameters from your code, it will work fine for you.
Note: Due to the Win32k.sys (User32/GDI32) Restrictions of Azure Web App sandbox, not every pdf conversion software can be installed on Azure WebApp as my did above. So PDFtk is a special software which not be implemented by using GDI.