In-loop filtering (ILF) is a key technology in video coding standards to reduce artifacts and enhance visual quality. Recently, neural network-based ILF schemes have achieved remarkable coding gains, emerging as a powerful candidate for next-generation video coding standards. However, the use of deep neural networks (DNN) brings significant computational and time complexity or high demands for dedicated hardware, making it challenging for general use. To address this limitation, we study a practical ILF solution by adopting look-up tables (LUTs). After training a DNN with a restricted reference range for ILF, all possible inputs are traversed, and the output values of the DNN are cached into LUTs. During the coding process, the filtering process is performed by simply retrieving the filtered pixel through locating the input pixels and interpolating between the cached values, instead of relying on heavy inference computations. In this paper, we propose a universal LUT-based ILF framework, termed LUT-ILF++. First, we introduce the cooperation of multiple kinds of filtering LUTs and propose a series of customized indexing mechanisms to enable better filtering reference perception with limited storage consumption. Second, we propose the cross-component indexing mechanism to enable the filtering of different color components jointly. Third, in order to make our solution practical for coding uses, we propose the LUT compaction scheme to enable the LUT pruning, achieving a lower storage cost of the entire solution. The proposed framework is implemented in the VVC reference software. Experimental results show that the proposed framework achieves on average 0.82%/2.97%/1.63% and 0.85%/4.11%/2.06% bitrate reduction for common test sequences, under the AI and RA configurations, respectively. Compared to DNN-based solutions, our proposed solution has much lower time complexity and storage cost.