Bottleneck to what? It is only recording checkpoints. It is not slowing down the forward advance of the DAG. It is orthogonal, except for the coinbases which can be spent into the DAG (after sufficient # of blocks to be probabilistically sure of coinbases not being reverted by an orphaned chain).
What is this blockchain supposed to checkpoint? DAG topology? Then this blockchain must possess fragmentation flexibility of DAG which is impossible in high-load, unless DAG waits for the blockchain to catchup. You can wait for 1 month before getting ability to spend coinbase coin, but once a corresponding checkpoint is recorded into the blockchain a greedy miner will generate another (better) tip containing a double-spending transaction invalidating tip which has been recorded.