Hi,
probably the best solution would be not to use SAP_ALL.
What value do you have in PRGN_CUST for key SAP_ALL_GENERATION? If it's set on 'ON' then SAP will regenerate SAP_ALL when you release your transports with new custom objects. Check note 439753.
1) They use same FM PRGN_CREATE_SAP_ALL. So no difference.
2) Not having record ADD_ALL_CUST_OBJECTS is taken as yes. Hence all custom objects will be included. The logic is opposite in case of ADD_S_RFCACL. Not having record in table is taken as NO. Hence S_RFCACL won't be included in SAP_ALL profile.
3) Importing transport into system should trigger regeneration of SAP_ALL unless you explicitly turn it off.
4) I am not sure I don't think that it will use DDIC if you execute it manually. It will use DDIC when regeneration is triggered during import of transport.
5) It's OK but as I said you should avoid using SAP_ALL profile.
Cheers