The reasons have been mentioned.
a)
Choice. The standards clearly state that all the TOC needs to do is test for colour vision. They may use ANY test they wish. B.2.1 clearly states that some have chosen to use the City Test. For the most part the choice to use one test over the others is down to cost. The other reasons for choosing the Ishihara have also been clearly highlighted. Nothing is preventing them from using a different test. They are making a choice to use the Ishihara.
b)
Further investigation needed. Again quite clearly highlighted in the standards document. B.2.5 states that if a defect is suspected; additional test can be used. B.2.5 also highlights that the Ishihara isn't usefull for Blue-yellow so again; an alternative test can be used.
c)
Flexibility. B.2.6 allows a TOC to allow for changes in technology and to allow flexibility in the workforce. A TOC could use the City test for all employees at the medical stage but for Driver specific they need to pass the Ishihara.
D)
Life events. Unfortunatly life happens to everyone. Different rules exist for those who are already employed and qualified. If a Driver had an accident and lost their colour vision then having to sit the Ishihara may be consider to be unfair. What does happen in all circumstances. The employee undergoes further investigation. B.1.4 allows the use of additional testing and 'specialist assessment'
E) One I'm going to chuck in myslef, which is blindingly obvious.
Dispute. If there was a dispute with the result or the way in which it was carried out, I have no doubt that the test will be retaken with a different practitioner and also that further testing would also take place if there was further dispute.
In the same document I linked there are 2 sets of guidleines.
I really really hope that help. :/