Within the framework of the implementation of Measure 18101 "Seismic Resistance of Systems and Building Structures" of the "Complex (Consolidated) Safety Upgrade Program" for NPP Power Units of the SE NNEGC Energoatom, a number of report documents were developed with the results of calculations of seismic resistance according to the approaches in NP 306.2.208-2016 "Requirements for seismic design and safety assessment of nuclear power plant units", PNAE G-7-002-86 "Standards for Calculating the Strength of Equipment and Pipelines of Nuclear Power Plants" and the HCLPF (High Confidence Low Probability of Failure) seismic margin value according to the approaches in the "Methods of the Design Calculation of the Seismic Resistance of Components of Operating NPPs within the seismic margin assessment (SMA) method MT-T.0.03.326-13". In accordance with the basic requirements of the SMA method, the determination of the HCLPF value was made on the basis of the stress-strain state (SSS) analysis for the zone with the maximum value of the seismic stress component (σS). However, in the framework of the state nuclear and radiation safety examinations of report documents of the SE NNEGC Energoatom, a number of calculation cases were detected where the above SMA method approach yielded insufficiently conservative HCLPF calculation results. It is currently relevant to determine the representative cross-sections of the design model of the elements for which the HCLPF value should be specified. This paper considers the example-based design case that demonstrated the insufficient conservatism of HCLPF calculation results in choosing a non-representative cross-section. Also considered are aspects of performing the analysis of the seismic margin resistance of NPP systems and elements with using specialized tools of modern computational complexes to eliminate errors in determining representative cross-sections.