JIT with the right settings can have a neutral to positive (speed up) effect on WHD'fyed games, but it's undocumented and unsupported. After a while, you grow tired of random artefacts and simply disable it.
whdload games are by definition launched by clicking an icon in WB mode since they are considered "installed". The only WHD'fyed bootable games I am aware of are games specially prepared for the CD32.
Well, what you gain in speed, you loose in accuracy. So it's all right to use old versions as long as you have that in mind.
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