Can both of these be used on the same weapon and stack for the limited purpose of bypassing DR?
For instance 4th Level Paladin has +3 heavy flail. She activates her Divine Bond and chooses to turn her weapon into a +4 heavy flail. She then casts Bless Weapon on the same heavy flail. For bypassing DR ONLY is it now considered a +5 weapon?
They are both classified as enhancement, but bless says it is not actually an enhancement bonus on a bonus to bypassing DR.
Also same Paladin with same weapon. If the she activates her Divine Bond to get flaming and then casts Bless Weapon is the item +3 Flaming for attacks but +4 for bypassing DR?
I think it pretty obvious the auto confirm for crits of Bless Weapon would apply in both circumstances.
No, any actual enhancement (even a +1) supersedes Bless Weapon's "treated as having a +1 enhancement".
Bless Weapon does not give you a +1 enhancement increase for bypassing DR, it is treated as a flat +1 for bypassing DR.
Put another way, Bless Weapon allows you to:
1) Bypass DR/Magic of evil creatures (the only thing +1 enhancement does vs DR).
2) Deal damage (the normal 1/2 damage) to evil incorporeal creatures (what a +1 enhancement does vs incorporeal creatures).
3a) The weapon becomes good aligned allowing you to bypass DR/Good (not related to the "treated as having a +1 enhancement").
3b) The weapon becomes good aligned allowing you to shut down Regen/Good (not related to the "treated as having a +1 enhancement").
4) Automatically confirms critical hits vs evil creatures (not related to the "treated as having a +1 enhancement").
In short, only clauses 3 and 4 matter on a weapon with a +1 enhancement and clause 3a doesn't matter on a weapon with a +4 enhancement.