[MIRROR] [NO GBP] Several pipe cap visibility fixes (#26900)

* [NO GBP] Several pipe cap visibility fixes (#81999)

## About The Pull Request

- Fixes cap overlays being added to turf even when pipe is not hidden.
- Fixes cap overlays being visible on turfs that are masked with
darkness plane, but still visible via mesons, cameras etc.

## Why It's Good For The Game

Seeing caps over “invisible” turfs via cameras, mesons, and other means
is actually a bug 'cause other pipes are hidden.

![amongus](https://github.com/tgstation/tgstation/assets/137328283/14ea7e70-1291-4487-b899-f4c4117c66c9)

## Changelog

🆑
fix: Fixed cap overlay being added even when pipe is not hidden.
fix: Fixed cap overlay being visible on turfs that are masked with
darkness plane, but still visible via mesons, cameras etc.
/🆑

* [NO GBP] Several pipe cap visibility fixes

---------

Co-authored-by: Interception&? <137328283+intercepti0n@users.noreply.github.com>

code/modules/atmospherics/machinery/atmosmachinery.dm

@@ -643,8 +643,10 @@
 	if(!has_cap_visuals)
 		return
 
-	var/turf/our_turf = get_turf(src)
-	our_turf.vis_contents -= cap_overlay
+	cap_overlay?.moveToNullspace()
+
+	if(!HAS_TRAIT(src, TRAIT_UNDERFLOOR))
+		return
 
 	var/connections = NONE
 	for(var/obj/machinery/atmospherics/node in nodes)
@@ -660,8 +662,8 @@
 	if(connections == NONE)
 		return
 
-	var/bitfield = CARDINAL_TO_PIPECAPS(connections)
-	bitfield |= ((~connections) & ALL_CARDINALS)
+	var/bitfield = CARDINAL_TO_PIPECAPS(connections) | (~connections) & ALL_CARDINALS
+	var/turf/our_turf = get_turf(src)
 
 	if(isnull(cap_overlay))
 		cap_overlay = new
@@ -672,12 +674,13 @@
 	cap_overlay.layer = layer
 	cap_overlay.icon_state = "[bitfield]_[piping_layer]"
 
-	our_turf.vis_contents += cap_overlay
+	cap_overlay.forceMove(our_turf)
 
 /obj/effect/overlay/cap_visual
-	appearance_flags = KEEP_APART
-	vis_flags = VIS_INHERIT_ID
+	mouse_opacity = MOUSE_OPACITY_TRANSPARENT
 	icon = 'icons/obj/pipes_n_cables/!pipes_bitmask.dmi'
+	vis_flags = NONE
+	anchored = TRUE
 
 /**
  * Called by the RPD.dm pre_attack()