David Stuart at Maya Decipherment argues that the design of the small site of Bonampak may have been directed towards the larger site of Yaxchilan. From hieroglyphic inscriptions it is known that Bonampak had strong political ties to Yaxchilan. These sites are 24 km apart and it is impossible to have a direct view of Yaxchilan from Bonampak since there is a high ridge in-between.
How it was possible to align distant sites with each other when there are hills and forest obscuring the sight is not explained by Stuart. One commentator (“Phil”) believes that Stuart suggests that the architects at Bonampak used a map (I do not believe this is what Stuart suggests). Phil brings up other sites or buildings that may be aligned across great distances such as Structure 1 at Calakmul which he claims is aligned towards El Mirador, 38 km away (I do not know if this is true, but let us assume that it is). It is believed that Late Formative Calakmul was in a subordinated position to El Mirador. The connection between the sites may have been maintained in the Early and Late Classic periods even if El Mirador was abandoned in the late Late Formative. There is one possible causeway connecting these two sites (and it may therefore be Late Formative in date). However, despite these connections, Phil has doubts of the mentioned alignments since only the tops of the summit temples would have been visible from each location. These summit temples are located 40-50+ m above the ground level and one would not have been able to see El Mirador from Calakmul from ground level where and when construction began.
However, you do not need a map to align buildings. Constructing linear alignments over great distances is not impossible even if the area in-between the connected locations is obscured by hills or the locations are not visible from the ground level. If major structures at El Mirador and Calakmul are aligned with each other they must have been so from the ground level (as no adjustment in alignment in constructions higher up on the pyramids are known to me).
I have discussed this problem for shorter distances (up to 3 km), which still is problematic when one has to connect preexisting sites with a forested area in-between. My case concerns the “triadic causeways” at Ichmul. The Central Acropolis at Ichmul dates back to at least the Early Classic. The roughly 3 km long causeways are Terminal Classic (some 300-400 years later) and connect the central part of Ichmul with three preexisting buildings located at three smaller sites. The causeways all aim towards a possible cenote/cave/flat area in central Ichmul, now covered by a church dedicated to the Black Christ. Unless there was a Prehispanic building located at this place, which the Spaniards completely dismantled, the point to which the three causeways would have been on ground level, not visible from the termini. One can indeed see the Black Christ church from each terminus but I doubt that any earlier possible building on the same spot as the church would have been as tall as the church towers.
I doubt that the usual “shouting method”, often used by workers when they locate their fellow workers some distance away and start cutting the forest from two directions to create linear paths in the vegetation (so-called brechas), is relevant across greater distances and particularly when one connect to already existing sites.
Using stars for alignment is perhaps another option but we do not need to get into the archaeostronomical stuff. There are far easier ways to align two points not visible from each others. Something visible from ground level that reaches great heights and is visible from great distances is smoke. The constructors at Bonampak may have used fire and smoke at Yaxchilan and a “smoking” way station on the hills to get the basic orientation. The same goes for Calakmul and El Mirador and the causeways at Ichmul. Another example is the Coba-Yaxuna causeway which aligns with several preexisting locations along its 100 km long trajectory. Straight brechas may have existed before the causeway but to align even the original brechas with preexisting sites one would need something possible to see from greater distances (and in the northern Yucatan the topography is far flatter than at Calakmul and for sure at Bonampak). Fires are also more visible in the dark than any star. Finding archaeological evidence for this hypothesis will not be easy.