It depends on how these assumptions have been recorded. If they had just written this within their description of an activity schedule item, then given the fact that the activity schedule is not Works Information this would not be something that the Contractor can claim for.
However, if as it appears here you have a very clear list of Contractor assumptions that the Employer has listed within the contract I would say this is different and now a contract document. Why include it if you can see that is what the Contractor has priced for if you the Employer intend to ignore it when it comes to assessing CE’s? Rightly or wrongly it would appear the Contractor has made it clear what they have allowed for, and the Employer has accepted this by a) accepting their bid and b) including these assumptions within the Contractors signed contract. This I would say would now be a compensation event - but not the cleanest way of dealing with it as you in effect have an ambiguity/inconsistency from day 1. Any such assumptions could/should have been dealt with one by one to make sure both Parties understand the associated liability with each of these items and incorporated within the contract accordingly rather than a separate list of assumptions.
Another cleaner way the Contractor could have dealt with this would have been a TQ (tender query) that everyone would have seen but everyone then understands the answer. Would the Employer entertain an alternative to the Works Information - if Yes that is what everyone prices, and if no then they know to price the higher spec. I know some Contractors might consider this affects their commercial advantage, but it takes away a potential ambiguity that they might practically if not contractually lose out on.