TRANSYT 16, TRANSYT 15 and TRANSYT 14: This issue is now redundant in these versions. You simply define the number of conflicts that you have and then set for each conflict, whether or not ALL the traffic is opposed or just a particular movement. Same flexibility also extends to the opposing traffic.
TRANSYT 13 and earlier: LOGICALLY you might think that setting two controlling links and then specifying that 100% of the traffic gives way to just the first link would be the same as specifying only one link in the first place. However, the TRANSYT model is affected by whether or not one or two controlling links are specified and hence TRANSYT may give slightly different results. Therefore, when specifying the number of controlling links in TRANSYT that a give-way has to give way to, only specify two controlling links if some or all of the give-way traffic gives way to both links.