Structural characterization in on-surface synthesis is primarily carried out by Scanning Probe Microscopy (SPM) which provides high lateral resolution. Yet, important fresh perspectives on surface interactions and molecular conformations are gained from adsorption heights that remain largely inaccessible to SPM, but can be precisely measured with both elemental and chemical sensitivity by Normal-Incidence X-ray Standing Wave (NIXSW) analysis. Here, we study the evolution of adsorption heights in the on-surface synthesis and post-synthetic decoupling of porous covalent triazine-phenylene networks obtained from 2,4,6-tris(4-bromophenyl)-1,3,5-triazine (TBPT) precursors on Ag(111). Room temperature deposition of TBPT and mild annealing to ~150 °C result in full debromination and formation of organometallic intermediates, where the monomers are linked into reticulated networks by C-Ag-C bonds. Topologically identical covalent networks comprised of triazine vertices that are interconnected by biphenyl units are obtained by a thermally activated chemical transformation of the organometallic intermediates. Exposure to iodine vapor facilitates decoupling by intercalation of an iodine monolayer between the covalent networks and the Ag(111) surface. Accordingly, Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS) and NIXSW experiments are carried out for three successive sample stages: organometallic intermediates, covalent networks directly on Ag(111) and after decoupling. NIXSW analysis facilitates the determination of adsorption heights of chemically distinct carbon species, i.e. in the phenyl and triazine rings, and also for the organometallic carbon atoms. Thereby, molecular conformations are assessed for each sample stage. The interpretation of experimental results is informed by Density Functional Theory (DFT) calculations, providing a consistent picture of adsorption heights and molecular deformations in the networks that result from the interplay between steric hindrance and surface interactions. Quantitative adsorption heights, i.e. vertical distances between adsorbates and surface, provide detailed insight into surface interactions, but are underexplored in on-surface synthesis. In particular, the direct comparison with an in-situ prepared decoupled state unveils the surface influence on the network structure, and shows that iodine intercalation is a powerful decoupling strategy.