This much depends on the project, the participating organisations and their internal rules and practices. It is always advisable that Beneficiary and partner organization would sign a partnership agreement regulating these issues.
In case of secondments money transfer concerns the cost category research and training, usually basing on real costs incurred by the organization, which hosts secondment (invoicing is good practice), the researcher usually is still employed by the beneficiary, who pays the allowances, the category management and indirect costs..
In case of Global fellowship – here partnership agreement is necessary. The researcher usually is still being paid by the sending institution (Beneficiary, according to the GA should employ the researcher for the whole duration of the project), but there some cases, where the TC institution is paying the researcher – in such a case allowances are transferred to TC. Cost category: Research & Training usually is transferred in total for the period of stay in TC (done according to the partnership agreement), transfer of management and indirect costs much depends on the partnership agreement.
So, as you can see this could differ from country to country, and from project to project and this much depends on the national law and internal regulations within the institution. What is important is that beneficiary is responsible that money should be spent for the project exclusively and allowances should be paid only for the benefit of researcher. That is why it is important to have partnership agreement regulating these issues.