If the tappets are the wrong way around, most likely one clearance will be more than it should be, and the other less than it should be or no clearance at all. The other possibility is that by luck, the two tappets are the same height and so the clearances are the same. If you had experience in this, I would suggest that you start the engine and listen to it, since a substantial difference between the two tappet sounds would be obvious. However since you are not accustomed to the sound, I do not think you would notice: you would just hear one tappet sound, and not be able to compare it with the usual two sounds.
Remember that to start the engine you must clamp the crankcase cover into position. After that if you have to remove the cover again because the tappets are the wrong way around, it is possible that your new gasket will be destroyed. This is additional to the possible replacement of the valve cover gasket.
If the tappets are the wrong way around, and as a result one of them has far too little clearance - or perhaps none - sustained running of the engine in that condition will cause one valve to burn, requiring another engine job to be done: lapping (if you are lucky) or replacing the burned valve. If you were unlucky, the valve seat would be damaged as well, requiring a somewhat more difficult replacement.
These risks are not unmanageable, and I think quite a few competent home repairers would "take the punt" and run the engine as it is - but those are people who would notice if it suddenly had uneven tappet sounds.
The decision is yours to make, Stuart. I am personally biased toward "doing the whole job" in cases like this because if you compromise the outcome to avoid removing those additional parts, you will end up being frightened of engine jobs in future. It is traditional to advise people who are thrown by a horse, to get back on it immediately and win the psychological battle with themselves.
