Made some tests - but still not sure that so it works.
When a stock shortage is generated, an entry in STOALL table is to be created. In this entry important is BESDAT and SEQ field value. 

On receipt, entries with the earliest date (BESDAT field), will be compensated as first.  In case there is more than one shortage in the same date, SEQ field value will be taken into account  - entry with highest SEQ value will be compensated as first. 

One complicating factor I found is that if we have multiple lines for the same product-site with different dates, AND we also have different PO lines scheduled out to bring stock in for them, and there's one SO line in the far future which we have not yet set up a PO line to cover, FUNAUTALL will create a shortage for that SO line.

Then, with SHTAUTFLG set as 2 (ie with the box ticked)  a new receipt will be allocated automatically to that distant future SO line rather than the earliest one. 

The solution appears to be either to set SHTAUTFLG to 1 (ie unticked) or to change the FUNAUTALL parameters (we run it as a batch task) so it does not generate, or prioritise, shortages.

Or reseller suggested SHTAUTFLG = 1 would work better for our business, but it might differ elsewhere. 

Hope that helps.