If you have 100+ tables - then you need a qlik developer who will write optimised script. Autogenerated scritp is for "dummies"- no offense - and allows people without script knowledge to do their own - simple things.
For such big scope you need someone who will know what to do and how to do it right, therefore answer to your question is one and only one - manual script writing!!
reason for my answer:
Your script will be understandable, structured and easier to maintain, it will execute much faster, right developer will use all know technics to speed it all up and on top of that i am sure that with autogenereted script you will not be able to achieve everything you need in this app.