True. Thats the downside of this approach. Maybe once every X days you can do a Stock Transfer, Material Issue and issue out this material and book the cost to a particular account head.
However, I would still take the valuation of the materials dropped into this warehouse as the total consumption of raw materials for this house, even though that value will still be showing up as Current Assets>Stock Assets>Virtual Warehouse.
In fact, I think it is acceptable from an accounting principle that till a house is sold, all the costs that have been associated with the house go towards the valuation of the house. The cost should, technically, be booked only when the house is sold.
So let’s say that there is a house that is finished, but not sold yet. I’d say that it is acceptable from an accounting principle that the cost of raw materials, labor and other expenses is included in the valuation of the finished goods stock item (the house).
Only when the house gets sold does this valuation move from the balance sheet (stock valuation of finished goods - the house) to the P&L account (cost of goods sold). ERPNext does this automatically.
If the client wants to actually book the costs, you can get the client to periodically (or just before Month End or filing of reports, etc.), pass a Stock Entry: Purpose Material Issue and book the Valuation of the Material issued to a particular project or cost center or account head.
The Manufacturing module as it gets enhanced will try and address your requirements here, but till such time, I think you can get very good and quality and actionable information using this approach.