How many Alternate Item Structures and Work Definitions can we support ?

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Hello,

My customer does Estimation of components, equipment resources, labor hrs, costing etc, based upon Customer drawings/documents (Bid)

While each order is different, there are largely similar and have slight Engg variations.  We are talking about 1000 Estimations per year across the company. When the End Customer provides the Order (Bid is Own) , the Estimation BOM ( Item Structure)  is transferred to a dedicated PDSC Org for Execution. 

We need ability to setup Alternate BOMs, Retrieve, Compare Alternate BOM , Link the Alternate BOM to the Alternate Routing (Work Definition). Modify the alternate BOM & Routings, perform cost roll up. I believe all these are possible but wanted to check if there are any known issues to be watch out.