HMRC are hot on this one .. the answer is "Yes = IF you are REALLY self-employed" ..
However from what you say, if HMRC investigates your workplace they may well decide you are not really self-employed at all (to be self-employed, essentially you need to have multiple 'clients' and on defined 'contracts' = i.e. work at different places for defined periods of time..).
(you can get some idea of the HMRC's point of view from link 1)
If they discover that you are still working at the same place, they are likley to come to the conclusion that your employer is (illegally) avoiding Tax (NI).
But if you don't claim for travel, they may well decide that YOU know you are not really self employed and hit you with a Tax (full NI) demand ... so I suggest you claim it but put some money aside in case of a dispute == if the HMRC want's to investigate your ex-employer, that's up to them ..
PS all the allowances and rates for the self-employed are set by HMRC == you REALLY should know what these are (link 2) :-)
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