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5-90 said:If you take the time to bleed the system properly, there's really no difference. What drilling does is allow you to not have to bleed the system manually - and it provides a small safety net if, say, you should get a compression leak into the cooling jacket (I've seen it happen on industrial equipment, and most of us use our rigs about the same way.)
Since you're supposed to leave some air space in the volume tank anyhow, you can just set the system up to bleed itself into that airspace. But, if you bleed properly (sounds like you do,) it's really not necessary - especially if you don't lose your head gasket! Once the system has purged itself of air, it shifts from "a useful two minutes" to "cheap insurance" for the 'just in case' eventuality.
You don't need to add an actual bleeder valve to complement it. If I were going to modify the engine casting proper, I'd probably look into doing a bypass around the thermostat ( Insert, Note that it does already have a bypass, see my comments below, it goes directly to the bottle side entrance) at 12:00 that would remain sealed - and do much the same thing. I just find it easier to drill out the flange, instead.
Neither idea is "right" or "wrong" - it's just what some people find easier to deal with than others. You probably automatically bleed the system after service, and have the time (even if it's only five to ten minutes) to do so. With my situation, I need to get jobs resolved as quickly as possible so I can move on to the next crisis...
A couple points of clarification. Mikeforte mentioned drilling the thermostat housing, not sure where that come from, unless there was a typo somewhere as there is no reason to drill the housing itself, unless he is calling a part of the thermostat itself a housing? If so it is confusing nomenclature since there is a seperate thermostat housing. Sorry to be picky, just trying to be real clear for future newbies!

The thermostat housing and engine block thermostat flange opening have a huge thermostat bypass that feeds the heater hose, 3/4" at that location, and when the heater hose is plumbed properly it pushes water constantly to the bottom of the heater core (5/8" hose) and to the upper side of the plastic bottle air - coolant separator (1/2" hose), thus flushing the thermostat housing's rear side of any air even when the thermostat is closed. This happens even before the thermostat opens, and continues with the thermostat open based on the elevation of all the parts involved.
With 2 bleed holes in the thermostat itself perhaps the air bleeds from the upper radiator hose backwards into the thermostat housing, then backwards through the top bleed hole, and then to the plastic bottle through the heater hose, but I think it would do this anyway once the thermostat opened, given enough air in the upper radiator hose.
Typically bleed holes in the thermostat are used to remove air from the bottom (or back) side of the thermostat so it can see, make physical contact with the liquid coolant, thus opening the thermostat on a timely basis. This is important in some engines, but the 4.0 in opinion based on my inspection of the physical design of the hardware yesterday, does not need the bleed holes, but what it does deperately need is to have the two heater hoses on the engine block plumbed properly to the water bottle!!!!!!!!
If it is plumbed improperly, i.e. heater hoses are attached backwards, all the thermostat holes in the world won't fix it, as it will continue to reintroduce air into the water pump. Lastly one should fill the system with coolant while the radiator upper hose is disconnected at the thermostat housing, and with the plastic bottle cap removed, as this will immediately remove 99% of any air in the block or the radiator during filling. Lastly, their are few warnings or picutures posted anywhere, if any, about how easy it would be to connect the heater hoses back wards at the engine block, near the thermostat housing, especially if you are not using OEM stealership hose sets. If not using the OEM hose set, there are two places where the one can connect the hoses backwards. The second place being at the metal hose T's or Y's.