The criteria that determine whether or not "penalties" are charged by HMRC depends very much on :
The amount of the evasion/avoidance
The nature (ie, type) of evasion/avoidance
The background circumstances (ie, was bona fide professional advice sought) which strongly advised or sanctioned/endorsed the action taken resulting in the outstanding tax/NI charges.
Any penalties are an additional sanction, over and above the established Tax/NI and non-negotiable interest calculated to the point at which the liabilities are settled. These are determined and are applied once the culpability and seriousness have been confirmed. HMRC will apply the penalties commensurate with the established position.
However, if, like in this case, it is absolutely clear that the amounts likely to be recovered from the liquidated entity are minimal or negligible, HMRC will take steps to reduce or negate the penalties position where there is no expectation of recovering any or very little at most. This, however, does not affect the levels of Tax/NI/Interest due on the original charges and has no impact on the circumstances where the liabilities arose in the first place. The charges arose due to the sole and specific actions of the entity itself.
Penalties applied by HMRC are additional, punitive measures applied subjectively depending on the specific circumstances. Similarly, HMRC can reduce or negate the same where there is little or no chance of recovery from the liquidated company and the remaining assets.
Only sayin' like.