The Mayor herself not being on board with the passage of the legislation as-is provides political cover for the federal Democrats. The Post article says, this may not be the best timing for the Council to make a Hold The Line For Home Rule stand, there may be a better hope in that the Council moots the issue by re-revising the proposal. Unfairly or not, standing hard on legislation like this gets perceived up on the Hill as daring them to do something about it.
(IIRC if the Congress is in-session during the next 10 business days after the bill is delivered to POTUS, he can just let it take effect by merely not vetoing it. No need to actively sign.)
A bit of a raw deal for the DC Council. A comprehensive Criminal Code reform even in a regular state is a legislatve PITA that turns into a multi-term slog with every possible stakeholder and interest group being on your case because they want their particular crime to either get cracked down on harder or be taken out of the criminal scope. All this, not providing you much near-term favorable political dividend.
If Congress acts, strictly legally it does not “violate Home Rule” since that whole apparatus is structured around that DC remains a dependency of Congress, who retain supremacy and power to intervene. But it still is a reminder of why the residents may want statehood.