Did you look at the A/F tables in the two tunes to compare them? If these tables are different the tunes will run different even if the F and L tables are identical. Do you realize that the L-Table, A/R table and F-Table are used all the time? The the F/L switch setting is used to move the center of the transition point. It is not a digital on/off switch.
An A/R of 30:1 during hard deceleration is not a problem. 15.5:1 is not a problem either if it occurs at light load and at some rpm, for example at a couple % throttle and 2,800 rpm or above. Now try that at 1,600 rpm, 4th or 5th gear, and gradually increasing the throttle and your EGT goes way up. The Dynojet POD is likely way too slow to accurately display quick transitions such as during down or up shifting. Also, O2 sensors don't reliably output a signal until the EGT is about 900F. This is most often higher then the engine runs at an idle. Thus idle and near idle fuel control is entirely table based. An O2 meter may display a value but it likely is bogus.
Higher A/F ratios run hotter up to the lean limit. However the throttle position determines the amount of air entering the engine. This means that if there is little air, there is a proportionate small amount of fuel. Thus with little air and fuel there is a small amount of heat. Imagine heating your valves with a butane cigarette lighter which reaches 2,400F or a propane blow torch that reaches perhaps 1,850F. The former produces perhaps 100BTU, the latter might produce 10,000BTU. Which one damages the cylinder head? Temperature is important, but the amount of heat is even more so.
The Triumph ECU can't use a wide band O2 sensor. Using the stock type O2 sensor, by checking the box in TuneECU, will have the ECU override the L and F table algorithm to adjust fueling to achieve that set in the A/F table. However, it will do so only in the narrow range it can read. Some modified tunes rely on having the O2 sensor on in order to control cruise A/F ratio. Others do not. Be aware that the process to get cruise and normal riding fueling really good is an intensive process. A dyno run is just a small part of it. Just ask Kevin what he is going through to get there.
TuneECU will reset the adaptation. DO NOT DISCONNECT it during the process as it also coordinates the primary TPS and idle control solenoid. The 12 minute tune only erases offsets in memory so that the bike starts relearning (adapting) from the base tune.
Whenever changing a tune, check the basics first: sync the TBs, check and set the primary TPS per manual if needed, make sure spark plugs are good, and that your coil connections are tight. Then load the new tune and ride to see how it works. Remember all tunes were created by someone you did not hire. The quality of the job, the goals to be met, and the motorcycle used are controlled by the buyer first and then the tuner selected. In essence you have been handed a "pig in a poke." No intention to deceive may be present, but you really don't know that what you are getting meets your expectations.