Vector rogue wave (RW) formation and their dynamics in Rabi coupled two-and three-species Bose-Einstein condensates with spatially varying dispersion and nonlinearity are studied. For this purpose, we obtain the RW solution of the two-and three-component inhomogeneous Gross-Pitaevskii (GP) systems with Rabi coupling by introducing suitable rotational and similarity transformations. Then, we investigate the effect of inhomogeneity (spatially varying dispersion, trapping potential and nonlinearity) on vector RWs for two different forms of potential strengths, namely periodic (optical lattice) with specific reference to hyperbolic type potentials and parabolic cylinder potentials. First, we show an interesting oscillating boomeronic behaviour of dark-bright solitons due to Rabi coupling in two component-condensate with constant nonlinearities. Then in the presence of inhomogeneity but in the absence of Rabi coupling we demonstrate creation of new daughter RWs co-existing with dark (bright) soliton part in first (second) component of the two-component GP system. Further, the hyperbolic modulation (sech type) of parameter along with Rabi effect leads to the formation of dromion (two-dimensional localized structure) trains even in the (1+1) dimensional two-component GP system, which is a striking feature of Rabi coupling with spatial modulation. Next, our study on three-component condensate, reveals the fact that the three RWs can be converted into broad based zero background RW appearing on top of a bright soliton by introducing spatial modulation only. Further, by including Rabi coupling we observe beating behaviour of solitons with internal oscillations mostly at the wings. Also, we show that by employing parabolic cylinder modulation with model parameter n, one can produce (n + 1) RWs. Our study reveals the fact that the spatially varying environment leads to the possibility of realization of two dimensional nonlinear structure in (1+1) dimensional setting.Spatially modulated two-and three-component Rabi-coupled Gross-Pitaevskii systems 2 features such RWs. Study of RWs has attracted significant attention not only in the more standard ocean-surface-dynamical problem [1,2], but also in other physical contexts. Indeed, there exists a vast amount of theoretical and experimental works on RWs in various fields ranging from optics [4, 6-9], Bose-Einstein condensates (BECs) [1,10], to plasmas [11], and atmospheric dynamics [12] (see also the recent short review [13]). Recently, high-order RWs [14] were excited successfully in a water wave tank. This suggests that a high-order analytic RW solution is of physical relevance and can be realized experimentally [14,15].These comprehensive theoretical and experimental studies on single component RWs, stimulated an increasing interest in investigating multi-component RWs. Rogue waves of the two-component Manakov system [16] have been studied extensively in the focusing regime [17,18] and in the defocusing regime [19][20][21]. The higher order RW solutions of the Manakov system ha...