issue with unmetrical notes

Those things are indeed a bit more tricky, and have multiple ways of solving them. I'll document my steps.

2nd system - bottom staff
Those three quarter notes for the bass seem quite evenly spaced (in the PDF) to me, which is why I decided to make them as a triplet. To create a triplet, one has to always start from the total duration it should occupy; so click on the G and then set the duration to a breve (8), thus matching the duration from the top staff.
Now go to "Add → Tuplets → Other…" and set the ratio of 3/8 (give us three things notated as the thing that would normally fit 8 times into the duration) whilst putting both the number and bracket format to "None". Now enter the F and the E.

We'll use the same triplet trick for the Tenor voice. Select start position, make it a breve (8), add a tuplet with ratio 3/8 without formatting. Then enter the notes within the tuplet: ← Q 5 E. Select the D at the start of the system and press + to restore the tie.

[optional] I think the intention is for these bottom notes to continue sounding whilst the soprano sings the "om" from "omnes". To do so, you can enter the notes and tie them from the triplet endnote, then mark those notes and the ties invisible instead of the invisible rest you currently have.
Likewise, I'd make the G in the bas (on "nes" of "omnes") a dotted note and hide the dot (or similarly, tie to an invisible 1/8th note. The tenor note will keep sounding due to the tie anyhow. So to that end, remove the slur you currently have and place a tie instead.

2nd system - top staff
First select the D and C in the soprano for "om" (of "omnes") and press X to flip their direction and force it upwards.

Now to the small notes. You'll want to make sure to use the "small" checkbox from the "Chord" section of the inspector and not the "Note" section. So for the C of omnes, you'll want to undo the small check for the note, then use the one for the chord instead. This will also scale the stem and flag accordingly.
However you'll notice the parenthesis overlapping the flag now (and imho being a bit close on the left side as well). To fix that, give the left parenthesis an X-offset of -0,10sp and the right one 0,80sp.
Then to the same for the A in "gentes".

3rd system
I'd indeed expect a (hidden) note to be required for the e-um syllable. The easiest way to add it given the current situation, is to use Insert mode. Which for just a single note you can do using the Ctrl+Shift modifier keys (Cmd+Shift on Mac).
Start by clicking on the A where the "um" from "e-um" will end up. Go into note input mode (N) and press Ctrl+Shift+A which will insert another 1/8th A right in front of the current beat. Mark the rests in the other voices invisible. Give the insert A the beaming the beam property single and also make it invisble