Company Act is applicable only to companies so Sec 141(3) disqualifies employees of company.
CA Act Cl 4 clarification is applicable to all entities so it disqualifies employees in all type of entities.
So there is difference between above 2,
Further these provisions are framed by different authorities at different time so it is not necessary they would have taken into considerations other things. CA Act, Regulations , Rules & its clarifications are pretty old and are little haphazard and issued by different people at different point of time, you cannot expect precision like DT / IDT here, there can be repetitions also, unless things are illogical accept them.
Further in case of ceiling limit first they specify, limit = number of partners x 20, so it is important to clarify if one of them is in full time employment his limit will be zero to avoid confusion.