If i understood correctly you are trying to build the CTS from pll_clk and this clk goes to divider (flops) and output of those divider will act as clock .
Then
1.why r u building the CTS from root pin to this divider flop if there is no other sink to the root clock except divider flop.
If there are other sinks to the root clk then you can specify divider flop CK pin as leafpin in your CTS spec file.
2. might be you can specify this divider flop as through point ----not a good idea