We usually recommend sticking exactly to the procedure as this is how the kit has been validated.
However if glass tubes for not available the use of polypropylene tubes should not cause any issues. However, heat transfer between glass and polypropylene tubes differ therefore incubation times may need to be extended slightly.
We recommend if any changes are made to the procedure the control should be run exactly as other samples. If the valued obtained for the control are the correct value, it is possible to conclude that the method deviation did not effect the performance of the assay.